how to simply extract the sequences of a gene list (~1000) in FASTA format from a sequence database (~400MB) in FASTA format generated by MAQ?
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Are you starting with a ~400MB FASTA file, containing ~1000 sequences, and you just want the list of sequence identifiers ("gene names")?
Try something like this at the Unix command line:
grep "^>" my_database.fasta
That string "^>" is a regular expression meaning look for any lines starting ("^") with the greater than symbol.
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Originally posted by johnsequence View PostThanks for reply. I actually need the IDs (headers) and sequences in FASTA format.
How is your list of identifiers stored? e.g. a text file with one id per line?
I would suggest you write a simple script, e.g. using Perl (perhaps with BioPerl) or Python (perhaps with Biopython), or your preferred script language.
Or, if you are happier just working at the command line, you can probably do this with EMBOSS seqret.
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You can use a couple of the utilities in the BLAST package from NCBI. Take your large FASTA file and create a BLAST database from it using formatdb. Then retrieve just the sequences you want from the BLASTdb using the fastacmd tool.
Code:%> formatdb -i <your.FASTA.file> -p F -n <your.blast.db> %> fastacmd -d <your.blast.db> -i <your.ID.file> > <output.file>
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