[EMBOSS] seqret problem?
pmr at ebi.ac.uk
Tue Jul 20 10:20:26 UTC 2004
Zhiqiang Ye wrote:
> hi all，
> I find that if there is a semicolon in the description line, seqret works wrong.
seqret works "correctly" ... but it is very confusing in this case.
The ">P1;" format is PIR format for a complete protein (fragemnts have
">F1;"). The rest of the line is the ID.
But in PIR format, the next line is the description - so EMBOSS will
read the first line of your sequence as a description, which is why it
appears on the first line of the FASTA format output.
You will find "seqret -sf pir" works the same way, and "seqret -sf
fasta" will complain about the sequence format.
I think there is no way to avoid this problem - because EMBOSS does not
know that the next line is not a sequence.
Hope that make things clearer,
MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI
SRWKGDFIPK MGMLLAVLEW GVEDEELAEL AKKVAHLLTK EKPQDCGNSF EA
[yezq at pro des]$ seqret test
Reads and writes (returns) sequences
Output sequence [z1bpc2.fasta]:
[yezq at pro des]$ more z1bpc2.fasta
>Z1BPC2 MELTSTRKKANAITSSILNR IAIRGQRKVA DALGINESQI
More information about the EMBOSS