FASTA program discussion list

[Rosemary Mantell <>]

Hi,

 

I have a question regarding FASTA output. I am running fasta36.exe with arguments ‘-q -m 10 -E 0.001 query.fasta targets.fasta’. When my ‘targets.fasta’ files contains a small number of sequences, I get a list of best scores in the output, followed by some alignments, such as the following:

 

>12CA:A ..
; sq_len: 260
; sq_offset: 1
; sq_type: p
; al_start: 78
; al_stop: 226
; al_display_start: 48
SVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHW
GSLDGQGSEHTVDKKKYAAELHLA-HWNTKYGDFGKAVQQPDGLAVLGIF
LKVGSA---KPGL--QKVVDVLDSIKTKGKSA-DFTNFDP--RGLLPESL
DYW---TYPGSLT---TPPLLECVTWIVLKEP-ISVSSEQVLKFRKLNFN
GEGEPEELMVDNWRPAQPLKNRQIKASFK

 

However, when ‘targets.fasta’ contains a large number of sequences, I find that only the best scores are printed and no alignment information (such as shown above) is printed. I’d like to be able to read this output using BioPython, so the change in file format is problematic. Is there some option I can use to control this output?

 

Thank you,

 

Rosemary

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