<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Don,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Many thanks for your comments and suggestions! Peter had already implemented most of the popular sequence formats in the original BioCocoa framework, but we'll have a look at your Java framework to see if we could add or improve relevant sequence formats in BioCocoa.</DIV><DIV>Again, many thanks for the feedback and keep up the good work!</DIV><DIV>Best wishes,</DIV><DIV>Alex</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On 14-jul-2006, at 19:16, don gilbert wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dear biococoa folks,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">> Finally, to come back to the question on the formats, perhaps we</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">> can learn from a classic sequence reader package called ReadSeq by</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">> d.g.gilbert.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">> I'm not sure where it can be found nowadays, so I put it</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">> temporarily on our server for you guys to download:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Readseq is available as it has been for ~ 15 years from</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="ftp://iubio.bio.indiana.edu/molbio/readseq/">ftp://iubio.bio.indiana.edu/molbio/readseq/</A><SPAN class="Apple-converted-space"> </SPAN>but see the readseq/java/ version</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">which I still update, but haven't had time recently to add new formats.<SPAN class="Apple-converted-space"> </SPAN>The</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">java version has more/better formats and documentation (and parser fixes),</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">but is also more complex than the C version.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The help document you list is from the 1992 C version, which I don't update.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Also,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">----------------</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">PUBLIC DOMAIN NOTICE:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">This software is freely available to the public for use. The</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">author, Don Gilbert, of Readseq and the Java package</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'iubio.readseq' does not place any restriction on its use or</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">reproduction. Developers are encourged to incorporate parts in</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">their programs. I would appreciate being cited in any work or</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">product based on this material. This software is provided without</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">warranty of any kind.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">> I guess we have most of them, except for IG, NBRF, Fitch, Zuker,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">> Olsen, ASN.1.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">With exception of NCBI's ASN.1, which requires also the NCBI toolkit</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">linked in with readseq, the others are essentially obsolete unless one</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">still uses old 1990's era molbio software (IG = Intelligenetics; NBRF = a PIR variant;</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Fitch from some classic molbio software (1970s? or 1980s) but a poor format;</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Zuker from Michael Zuker's MULFOLD rna folding software, Olsen from Gary Olsen's</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phylogeny software).</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please use readseq as desired,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Don Gilbert</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">oat.% readseq</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Readseq version 2.1.24 (24-May-2006)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Readseq version 2.1.24 (24-May-2006)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Read & reformat biosequences, Java command-line version</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Usage: java -cp readseq.jar run [options] input-file(s)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>For more details: java -cp readseq.jar help more</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Options</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-a[ll]<SPAN class="Apple-converted-space"> </SPAN>select All sequences</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-c[aselower]<SPAN class="Apple-converted-space"> </SPAN>change to lower case</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-C[ASEUPPER]<SPAN class="Apple-converted-space"> </SPAN>change to UPPER CASE</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-ch[ecksum] <SPAN class="Apple-converted-space"> </SPAN>calculate & print checksum of sequences</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-degap[=-]<SPAN class="Apple-converted-space"> </SPAN>remove gap symbols</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-f[ormat=]# <SPAN class="Apple-converted-space"> </SPAN>Format number for output,<SPAN class="Apple-converted-space"> </SPAN>or</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-f[ormat=]Name<SPAN class="Apple-converted-space"> </SPAN>Format name for output</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>see Formats <SPAN class="Apple-converted-space"> </SPAN>list below for names and numbers</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-inform[at]=# <SPAN class="Apple-converted-space"> </SPAN>input format number,<SPAN class="Apple-converted-space"> </SPAN>or</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-inform[at]=Name<SPAN class="Apple-converted-space"> </SPAN>input format name.<SPAN class="Apple-converted-space"> </SPAN>Assume input data is this format</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-i[tem=2,3,4] <SPAN class="Apple-converted-space"> </SPAN>select Item number(s) from several</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-l[ist] <SPAN class="Apple-converted-space"> </SPAN>List sequences only</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-o[utput=]out.seq <SPAN class="Apple-converted-space"> </SPAN>redirect Output</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-p[ipe] <SPAN class="Apple-converted-space"> </SPAN>Pipe (command line, < stdin, > stdout)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-r[everse]<SPAN class="Apple-converted-space"> </SPAN>reverse-complement of input sequence</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-t[ranslate=]io <SPAN class="Apple-converted-space"> </SPAN>translate input symbol [i] to output symbol [o]</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>use several -tio to translate several symbols</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-v[erbose]<SPAN class="Apple-converted-space"> </SPAN>Verbose progress</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-compare=1<SPAN class="Apple-converted-space"> </SPAN>Compare two sequence files, reporting differences (flags=nodoc,noid,nolen,nocrc)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-amino[translate] <SPAN class="Apple-converted-space"> </SPAN>translate dna to amino acids</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Documentation and Feature Table extraction:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-feat[ures]=exon,CDS... <SPAN class="Apple-converted-space"> </SPAN>extract sequence of selected features</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-nofeat[ures]=repeat_region,intron... remove sequence of selected features</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-field=AC,ID...<SPAN class="Apple-converted-space"> </SPAN>include selected document fields in output</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-nofield=COMMENT,... remove selected document fields from output</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-extract=1000..9999<SPAN class="Apple-converted-space"> </SPAN>* extract all features, sequence from given base range</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-subrange=-1000..10<SPAN class="Apple-converted-space"> </SPAN>* extract subrange of sequence for feature locations</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-subrange=1..end</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-subrange=end-10..end+99</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-pair=1<SPAN class="Apple-converted-space"> </SPAN>* combine features (fff,gff) and sequence files to one output</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-unpair=1<SPAN class="Apple-converted-space"> </SPAN>* split features,sequence from one input to two files</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Pretty format options:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-wid[th]=#<SPAN class="Apple-converted-space"> </SPAN>sequence line width</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-tab=#<SPAN class="Apple-converted-space"> </SPAN>left indent</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-col[space]=# <SPAN class="Apple-converted-space"> </SPAN>column space within sequence line on output</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-gap[count] <SPAN class="Apple-converted-space"> </SPAN>count gap chars in sequence numbers</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-nameleft, -nameright[=#] <SPAN class="Apple-converted-space"> </SPAN>name on left/right side [=max width]</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-nametop<SPAN class="Apple-converted-space"> </SPAN>name at top/bottom</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-numleft, -numright <SPAN class="Apple-converted-space"> </SPAN>seq index on left/right side</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-numtop, -numbot<SPAN class="Apple-converted-space"> </SPAN>index on top/bottom</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-match[=.]<SPAN class="Apple-converted-space"> </SPAN>use match base for 2..n species</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>-inter[line=#]<SPAN class="Apple-converted-space"> </SPAN>blank line(s) between sequence blocks</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">This program requires a Java runtime (java or jre) program, version 1.1.x, 1.2 or later</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The leading '-' on option is optional if '=' is present.<SPAN class="Apple-converted-space"> </SPAN>All non-options</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(no leading '-' or embedded '=') are used as input file names.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">These options and call format are compatible with the classic readseq (v.1992)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">* New experimental feature handling options, may not yet work as desired.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To test readeq, use: java -cp readseq.jar test</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Known biosequence formats:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>ID<SPAN class="Apple-converted-space"> </SPAN>Name <SPAN class="Apple-converted-space"> </SPAN>Read<SPAN class="Apple-converted-space"> </SPAN>Write<SPAN class="Apple-converted-space"> </SPAN>Int'leaf<SPAN class="Apple-converted-space"> </SPAN>Features<SPAN class="Apple-converted-space"> </SPAN>Sequence<SPAN class="Apple-converted-space"> </SPAN>Suffix<SPAN class="Apple-converted-space"> </SPAN>Content-type</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>1<SPAN class="Apple-converted-space"> </SPAN>IG|Stanford<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.ig <SPAN class="Apple-converted-space"> </SPAN>biosequence/ig</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>GenBank|gb <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.gb <SPAN class="Apple-converted-space"> </SPAN>biosequence/genbank</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3<SPAN class="Apple-converted-space"> </SPAN>NBRF <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.nbrf <SPAN class="Apple-converted-space"> </SPAN>biosequence/nbrf</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>4<SPAN class="Apple-converted-space"> </SPAN>EMBL|em<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.embl <SPAN class="Apple-converted-space"> </SPAN>biosequence/embl</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>5<SPAN class="Apple-converted-space"> </SPAN>GCG<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.gcg<SPAN class="Apple-converted-space"> </SPAN>biosequence/gcg</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>6<SPAN class="Apple-converted-space"> </SPAN>DNAStrider <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.strider<SPAN class="Apple-converted-space"> </SPAN>biosequence/strider</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>7<SPAN class="Apple-converted-space"> </SPAN>Fitch <SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.fitch<SPAN class="Apple-converted-space"> </SPAN>biosequence/fitch</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>8<SPAN class="Apple-converted-space"> </SPAN>Pearson|Fasta|fa <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.fasta<SPAN class="Apple-converted-space"> </SPAN>biosequence/fasta</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>9<SPAN class="Apple-converted-space"> </SPAN>Zuker <SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.zuker<SPAN class="Apple-converted-space"> </SPAN>biosequence/zuker</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>10<SPAN class="Apple-converted-space"> </SPAN>Olsen <SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.olsen<SPAN class="Apple-converted-space"> </SPAN>biosequence/olsen</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>11<SPAN class="Apple-converted-space"> </SPAN>Phylip3.2<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.phylip2<SPAN class="Apple-converted-space"> </SPAN>biosequence/phylip2</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>12<SPAN class="Apple-converted-space"> </SPAN>Phylip|Phylip4 <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.phylip<SPAN class="Apple-converted-space"> </SPAN>biosequence/phylip</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>13<SPAN class="Apple-converted-space"> </SPAN>Plain|Raw<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.seq<SPAN class="Apple-converted-space"> </SPAN>biosequence/plain</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>14<SPAN class="Apple-converted-space"> </SPAN>PIR|CODATA <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.pir<SPAN class="Apple-converted-space"> </SPAN>biosequence/codata</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>15<SPAN class="Apple-converted-space"> </SPAN>MSF<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.msf<SPAN class="Apple-converted-space"> </SPAN>biosequence/msf</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>16<SPAN class="Apple-converted-space"> </SPAN>ASN.1 <SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.asn<SPAN class="Apple-converted-space"> </SPAN>biosequence/asn1</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>17<SPAN class="Apple-converted-space"> </SPAN>PAUP|NEXUS <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.nexus<SPAN class="Apple-converted-space"> </SPAN>biosequence/nexus</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>18<SPAN class="Apple-converted-space"> </SPAN>Pretty<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.pretty<SPAN class="Apple-converted-space"> </SPAN>biosequence/pretty</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>19<SPAN class="Apple-converted-space"> </SPAN>XML<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.xml<SPAN class="Apple-converted-space"> </SPAN>biosequence/xml</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>20<SPAN class="Apple-converted-space"> </SPAN>BLAST<SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.blast<SPAN class="Apple-converted-space"> </SPAN>biosequence/blast</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>21<SPAN class="Apple-converted-space"> </SPAN>SCF<SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.scf<SPAN class="Apple-converted-space"> </SPAN>biosequence/scf</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>22<SPAN class="Apple-converted-space"> </SPAN>Clustal<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.aln<SPAN class="Apple-converted-space"> </SPAN>biosequence/clustal</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>23<SPAN class="Apple-converted-space"> </SPAN>FlatFeat|FFF <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>.fff<SPAN class="Apple-converted-space"> </SPAN>biosequence/fff</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>24<SPAN class="Apple-converted-space"> </SPAN>GFF<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>.gff<SPAN class="Apple-converted-space"> </SPAN>biosequence/gff</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>25<SPAN class="Apple-converted-space"> </SPAN>ACEDB<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>yes<SPAN class="Apple-converted-space"> </SPAN>--<SPAN class="Apple-converted-space"> </SPAN>-- <SPAN class="Apple-converted-space"> </SPAN>yes <SPAN class="Apple-converted-space"> </SPAN>.ace<SPAN class="Apple-converted-space"> </SPAN>biosequence/acedb</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>(Int'leaf = interleaved format; Features = documentation/features are parsed)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-- gilbertd@indiana.edu -- <A href="http://marmot.bio.indiana.edu">http://marmot.bio.indiana.edu</A>/</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Biococoa-dev mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Biococoa-dev@bioinformatics.org">Biococoa-dev@bioinformatics.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="https://bioinformatics.org/mailman/listinfo/biococoa-dev">https://bioinformatics.org/mailman/listinfo/biococoa-dev</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">___________________________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">$0 Web Hosting with up to 200MB web space, 1000 MB Transfer</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">10 Personalized POP and Web E-mail Accounts, and much more.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Signup at <A href="http://www.doteasy.com">www.doteasy.com</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> </BLOCKQUOTE></DIV><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>** Alexander Griekspoor **</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>The Netherlands Cancer Institute</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Department of Tumorbiology (H4)</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Plesmanlaan 121, 1066 CX, Amsterdam</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Tel:<SPAN class="Apple-converted-space"> </SPAN>+ 31 20 - 512 2023</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Fax:<SPAN class="Apple-converted-space"> </SPAN>+ 31 20 - 512 2029</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>AIM: <A href="mailto:mekentosj@mac.com">mekentosj@mac.com</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>E-mail: <A href="mailto:a.griekspoor@nki.nl">a.griekspoor@nki.nl</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Web: <A href="http://www.mekentosj.com">http://www.mekentosj.com</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Microsoft is not the answer,</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Microsoft is the question,</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>NO is the answer</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************</FONT></P> </DIV><BR></DIV></BODY></HTML>