[meltsim] Re: [Fwd: [meltsim] Information]
J.W. Bizzaro
jeff at bioinformatics.org
Wed Dec 5 10:23:13 EST 2001
Carla Clemente wrote:
>
> I have a DNA sequence but I can´t understand how MeltSim 1.0-Compile
> works. Could you send me a test sequence to practice with and give me an
> explain about this command.
Compile is not neccessary to run Melt, the program that actually generates a
melting curve. Melt accepts "raw" DNA sequences (ACGATAGACAGT... without
annotation).
Compile is an auxilary program written to extract raw sequences from
annotated GenBank documents. Attached is a file with 2 GenBank docs. In
Compile, open the file using the menus, then select the feature (see below)
that you want extracted (in the box at the top of the window). Next, select
Compile>Run in the menus.
What do I mean by feature? Look at what is written under the FEATURES
section in the GenBank doc. You'll see "source", "CDS", "gene", etc. And
then to the right, you'll see the sequence interval identified (e.g.,
"3590..4284"). If you select the feature "CDS", as an example, Compile will
take the sequence from 1 to 178 in the first document and put it in a
separate file, and it will do that everywhere it finds CDS identified (it
happens to be only once in the attached file). The result will be a file
with raw *CDS* DNA sequences.
Cheers.
Jeff
-------------- next part --------------
LOCUS AF269155 178 bp DNA INV 20-JUL-2001
DEFINITION Anopheles gambiae transcription factor Deformed (Dfd) gene, partial
cds.
ACCESSION AF269155
VERSION AF269155.1 GI:9652094
KEYWORDS .
SOURCE African malaria mosquito.
ORGANISM Anopheles gambiae
Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
Pterygota; Neoptera; Endopterygota; Diptera; Nematocera;
Culicoidea; Anopheles.
REFERENCE 1 (bases 1 to 178)
AUTHORS Powers,T.P., Hogan,J., Ke,Z., Dymbrowski,K., Wang,X., Collins,F.H.
and Kaufman,T.C.
TITLE Characterization of the Hox cluster from the mosquito Anopheles
gambiae (Diptera: Culicidae)
JOURNAL Evol. Dev. 2 (6), 311-325 (2000)
MEDLINE 21150895
PUBMED 11256376
REFERENCE 2 (bases 1 to 178)
AUTHORS Powers,T.P. and Kaufman,T.C.
TITLE Direct Submission
JOURNAL Submitted (09-MAY-2000) Biology, HHMI-Indiana University, 1001 E.
Third St., JH A003, Bloomington, IN 47405-3700, USA
FEATURES Location/Qualifiers
source 1..178
/organism="Anopheles gambiae"
/db_xref="taxon:7165"
/dev_stage="adult"
gene <1..>178
/gene="Dfd"
CDS <1..>178
/gene="Dfd"
/codon_start=2
/product="transcription factor Deformed"
/protein_id="AAF91400.1"
/db_xref="GI:9652095"
/translation="PKRQRTAYTRHQILELEKEFHYNXYLTRRRRIEIAHTLVLSERQ
IKIWFQNRRMKWKKD"
BASE COUNT 65 a 36 c 38 g 38 t 1 others
ORIGIN
1 accgaagcgg caaaggacgg cttatacccg ccatcaaata ttagagctag aaaaagagtt
61 tcattataat ngttacctta cacgacgccg acggatagaa atagctcata cgcttgttct
121 ttcggaacga cagataaaaa tctggtttca aaacagacgc atgaagtgga aaaaggac
//
LOCUS AF170022 5069 bp DNA INV 24-APR-2001
DEFINITION Anopheles gambiae clone I29 genomic sequence.
ACCESSION AF170022
VERSION AF170022.1 GI:6671106
KEYWORDS .
SOURCE African malaria mosquito.
ORGANISM Anopheles gambiae
Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
Pterygota; Neoptera; Endopterygota; Diptera; Nematocera;
Culicoidea; Anopheles.
REFERENCE 1 (bases 1 to 5069)
AUTHORS Hill,S.R., Leung,S.S., Quercia,N.L., Vasiliauskas,D., Yu,J.,
Pasic,I., Leung,D., Tran,A. and Romans,P.
TITLE Ikirara insertions reveal five new Anopheles gambiae transposable
elements in islands of repetitious sequence
JOURNAL J. Mol. Evol. 52 (3), 215-231 (2001)
MEDLINE 21321255
REFERENCE 2 (bases 1 to 5069)
AUTHORS Hill,S.R., Leung,S.S., Quercia,N.L., Vasiliauskas,D., Yu,J.,
Pasic,I., Leung,D., Tran,A. and Romans,P.
TITLE Direct Submission
JOURNAL Submitted (19-JUL-1999) Zoology, University of Toronto, 25 Harbord
Street, Toronto, Ontario M5S 3G5, Canada
FEATURES Location/Qualifiers
source 1..5069
/organism="Anopheles gambiae"
/strain="G3"
/db_xref="taxon:7165"
/clone="I29"
repeat_region <1..2793
/rpt_family="transposon Guildenstern"
/rpt_type=dispersed
repeat_region 2786..2890
/note="degenerate; similar to Ikirara1 inverted repeat in
GenBank Accession Number U55049"
/rpt_type=inverted
repeat_region 2786..4707
/rpt_family="transposon Ikirara"
/rpt_type=dispersed
repeat_region 3009..3580
/note="truncated"
/rpt_family="transposon Vash2"
/rpt_type=dispersed
gene 3590..4284
/gene="Pif1-like"
/pseudo
repeat_region 4512..4707
/note="truncated; similar to Ikirara1 inverted repeat in
GenBank Accession Number U55049"
/rpt_type=inverted
BASE COUNT 1312 a 1274 c 1331 g 1152 t
ORIGIN
1 gtcgaccgac agaaagcatg cattcggtgt ggagcagaag gccacttggc taaagactgc
61 aacgccaagg tgaagtgcgc cgtgttcagt ggtcctcatc gcgtcggcca cagagattgt
121 gtacgcccca tgctgcgatg tcctcacaaa gggtacttca actcaatgtg gatcattgtc
181 gggaaggaca gggcctagca ctgcaatccg cgcgggaaca tcgtgctgat gtcctgatct
241 tgtcggacat gtttacgcct cccaacaaca aagggcgatg ggcatacgac gcatcaagaa
301 aagtagctat agtagccacc ggctcctacc caatacaacg ggtatggggc tgtacagtgc
361 cgggactggt ggctgctaaa gtggccggga tcatctttat cagcgtctac gtcctccgag
421 cctatctcca caggaatacg agcggctcct tgaggccgtt gagctggagg cctcatccca
481 ctcccacgtc gtgatcgttg gtgatttcaa tgcttggcac acggaatggg gtagcagacg
541 caataacctg cgtggcgagg aattactgca gatggtggag gtgctgggac tctccatcct
601 caatagtggc agcgcaccga cgttcatcgg cagaggagca gcaaggccca gtgtcattga
661 cgtgaccttc gcaactccgt cgctagtact gcatgacacc cgggaggtac tagatttcgc
721 cagatacgac caccagctga tccggttcga gacaaaaagc cctgcactgg ccgcaaggag
781 agttcagctt tcccagcgga atcggtcgca gcaacggtct ccccgccgtg attcaccaat
841 caaccggcag cacacttcat gtgccggtag gaggtggaaa actaaacaat tcagcgaaaa
901 ttctttcctc ctagcactca gagacgtgaa cttcgccgag caagctgtga ctgatgcgga
961 tatagtcgag acgcccaggg aaatgcagga tatagcccac cagatagcaa caaggaaggc
1021 accaggactt gatggaattc ccaacgccgc ggtgaaggcg cgatcgggat gtatccggat
1081 gttttttgca gaatgtacca ggactgctta actcgtggca cgtttccgtc cgagtggaag
1141 cgccagcgcc tcgtactgct tccgaagacg ggcaaaccac ccggggaaag cagctcatat
1201 cggccgctgt gcatgctcga cgcactcggc aaggtattgg agcgactaat cctgaaccgc
1261 ctcaacaagc atctcgtgtt gtagacgcag ggagaagggc caagtaccaa caatcgcgac
1321 aagcgctgtc tgatggtggt cgcattggat attcgcaacg cgttcaaccc cgctatttga
1381 cagtctatag ctgatgcgtt gcggaataaa ggggtcccat cagcgcttct aaatatatta
1441 ggaagctact tcgaggaacg caagctgata tacaacacca gcgcgggccc ggtcgagcgt
1501 catatcagcg cgggagttcc acaggggtcc agcttgggcc cgaccctgtg gaacgtgatg
1561 tacgacggag tcttggcgtt gagctaccaa ctggggcgga acttatcggc tatgcatgac
1621 ctcgttttgc tggctccagg tacaacgccg gcagcagcag tagtagtagc tgaggaagct
1681 gtgtcagcag tagaccggtg gctgcgcgag catcacttgg agctcgcaca tgcgaaaacg
1741 gagatgacgg tgatctctag cctgcagcag cctccggagg acatcaccat cactgtggga
1801 ggtacagtgg tgccgttctc gcgtaccctc aaatacctcg gggtacgctt acactacaac
1861 ctgtcgtggg ttcctcatgt gaaggcggtt attcagaagg caacgcagat agtacaggcg
1921 gtcacacgat tgatgccgaa ccaccgagga ccaaagacgt cacgatgccg cttgcttgca
1981 gcggttaccg actcgacaat gcgatacgct gcacctgtct ggcacggagc cttgactaac
2041 cgagagtgcc gcagtctgct aaagcgcgtg cagtgaaagg cagcgatcgc gtggctcgaa
2101 cgttccggac ggtaaggtat gagaccgccg tgctgctcgc gggactggtg ccaatctgca
2161 gagccgtagc ggaggacacc cgagttcaca gcagacgcgg gaccggtgta agtagcagcg
2221 agctacggaa agaggagcga cagcggacta ttgaagagtg gcagacgact tgggatgcag
2281 acgccgtagc agacaacgcc agcagatatg tcaggtgggc acaccacgta attccggacg
2341 tgggagcctg gcagttgggg aatcacggag aggtacgttt catttgtctc aggtgttgtc
2401 aggacacgga tttttccgcg aatacctgaa caaaatgaga ttcacctcat ctccagcctg
2461 cactcgttgc cctggtgtag tcgagggagt agaacatgta atgttcgaat gccttcgctt
2521 tgctgaggtg aggagtgagc tattggatgg agttttgcca gaaacgttgg aggcgcacat
2581 gcttcaatca cccaccaact ggaccaacgt gtgcgaggcc gccaagcgca tcacctcaga
2641 actccaacgc tgctgggacg aggaacgcgc cattctcggc gcacaggcca tgctggagga
2701 acccgccaat cgactcgacc ccgaagcagt ccggcgtacc cgaatgacct tcgaaatgta
2761 gctagaagga cgcagacgca actttttcag atatcatcaa cgatttcaag catcataccg
2821 caatcttggc tttggctaag acagattcgg gaagggataa cgcggtcttg atataaagtg
2881 taaaaccctg taacatcccc tccccctaga ctcctcgcgg ggcacagggg aaggggcagg
2941 aagagggttg gggaatatgt aaatattgta aatttactga aataaactaa cacgattgtt
3001 aaaaaaaagc atctactcgg gcacttgcgc ggctagagtc catccaacgg aaggcaacgc
3061 gcttcgccct tcgtgattgg ccgcgtcgtc tcgactacag aactagatgt ttgctgcttg
3121 ggatcccgcc tctcgccgaa cgtgttgagc acaccagact ggcatttatc acgggaatct
3181 taaaccttaa atggtcttaa atcttaatct taatcttaaa tggttcccat cgactgtccc
3241 gagctgcttt caaggattca cctttatgtt cctgccagaa tactccgtcg ccgaacaatg
3301 ctggcagtcg ctgaaacccg aacaacattt ggctctcgca attcgttctt tgtatgtgcc
3361 gtctattaaa ttcagctgac gatatttacg agcctggaat gacgataacg gaactgactt
3421 cacttttaag tgttcggaat gcgttcaaca ataacaatat ataatgttct gttctttatg
3481 taatgtgtat tgtaaacaaa ttttgactcg agaggcttca tagtccatcg attaataaac
3541 taaactaaac taaacttaac taaactaaac taaactaaac taaataataa tgtttgtggg
3601 tggccagtat taagtacctt tacaagtacg tgcataaggg acatatcagc atatcagccc
3661 tggcaatcat cttcggtttt gagatgcagg caaaaacagt cactgtcgtc gtactaccga
3721 tacacctcga gaacaaccag ggcatcgtct ttaattcgaa cgaaaacatc gaatcggtca
3781 tcgaacgagg ccaccacaca atgctaacgc gcttctttca gctgatggca aacgatcctt
3841 gcgcgtgaaa tttcacaaat caagagctac cgacgtactt cagatatgcc aagccagcga
3901 cttccatggc atgaaggttc aggatgccag tggattcaac gcattcgtga agtaagcatc
3961 gtgatttgtc gtatggtata ctgtccgatg tcgcagatgg aacggtactg cttgcggttg
4021 ttgctgtgct gatcgcaagg gcccaacttc attagaagac cttcggatgg ttgacgctaa
4081 gtttatgcga cttaccatga agcagctact atggatagga tgctacaaga tgactatgaa
4141 tgggatcggg caatgcagga agccgttccg ttccatatgc cttctcaact gcgccatctg
4201 ttcgcagtca tcctgtcgca agagccacaa catcctcgcc gcctgtggga gttgtacgtg
4261 ttacattttt gtgagggttt ccattagcag catcgagata caacgcagaa ctctgatcaa
4321 aacatgctgc tgcgtacaca ggagtaattt ggtgctctgc gcgtcattgg cagatacttg
4381 cgccaattga caccatcaaa aacgctgatc aagtttccgg acatgccact attggctgat
4441 tttcaacctc ttccgatgca ccttcaatcc gatcatggta acgatgtaaa atcgcagatc
4501 gatgcagatc gtccgtgtaa aaaaatattc gaccgcatgt cctcggcgcg gaccagtgtg
4561 ttcgagaaat gtgccgcaga ttcagcactg catccgatga attcaggtat catcaacgtt
4621 ttcaagcatc ataccgcagt cttggctttg gctaagacag attcgggaag gggtcccgcg
4681 gtcttgagat aaagtgtgaa aacctgtaat gccgacgtga ggaagttggt aaagtgagtt
4741 tatccgaact tagggtggca ttatcgaaaa gcggaatatt tcacagatcg agcaatactc
4801 ttgtggtgat cagcgccatc tgcacatcag atgccgcaat ctcaacgtcg ctgtcatatt
4861 caccacctta agtggacatc accttgtggt atagcgtaag ttgagttgac agatattaga
4921 tcagtttagt gcaggacgaa cgaggaagca gcgatcggat gtgccgatcg ctcgttcact
4981 tctctcgcaa ccatccgccg attcggatca attaatacgt tgttaataat tagttgtgaa
5041 taataaagat aagctccgac taaaagctt
//
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