Config file for PROT4EST created Sun Dec 19 13:47:47 GMT 2004


For help on any of these please consult the README file

#Full path to fasta input file, e.g. /home/joe/EST/rubellus.fsa
1.   Input File [fasta format]:/home/jamesw/PartiGene/brugia/BMC.fsa

#prot4EST will create this directory, e.g. 'output' will be created in the
#directory p4e is launched from
2.   Output Directory:out_brugia

#e.g. Lumbricus rubellus
3.   Organism Name (full):Brugia malayi

4.   Location of genetic code file: /usr/local/ncbi/data/gc.prt 

#Fasta and BLAST files containing these sequences are included in the prot4EST release.
#Enter the full path.
5.   Ribosomal RNA BLAST database:/usr/local/ncbi/db/rRNA.fsa
6.   Mitochondria BLAST database [protein]:/usr/local/ncbi/db/mito_metaNfungi.fsa

#The defaults are shown
7.   Evalue for rRNA search (BLASTN): 1e-65
8.   Evalue for BLASTX: 1e-8

#If you have previous carried out BLASTx search on these sequences then enter the path to the report file
#or directory containing only these files
#If left blank then prot4EST assumes you wish to carry out a BLASTx search on these sequences
#You are advised to read the userguide regarding this option
9.    Location of pre-computed BLASTX report files/directory:/home/jamesw/PartiGene/brugia/blast_reports/

#Fill in all entries for 9a-c OR just 9d (if DECODER has already been run on these sequences)
#e.g. /home/joe/partigene/protein
10a.  Path to sequence and quality files [protein directory]:
#defaults shown
10b.  Suffix for EST sequence files: seq
10c.  Suffix for EST quailty files: qlt
	 or
10d.  Path to pre-computed DECODER results:

11. ESTScan Matrix File [optional]:

12. Codon Usage Table (gcg format) [optional]:/home/jamesw/PartiGene/brugia/Bm.cod


For help on any of these please consult the user guide
