The NeedlemanWunsch alignment crashes on certain sequences
Hi all,
I have two lists of sequences and I need to calculate the similarity for every pair from these two lists. So I apply 'needle' from EMBOSS package. Everything goes fine until this sequence comes across: 'IDMSAYPVESIR'. When it happens the program crashes with the message:
Warning: Sequence 'embl::ref.txt:EMBOSS_001' has zero length, ignored
Error: Unable to read sequence 'seq1.txt'
Died: needle terminated: Bad value for '-asequence' and no prompt
Can anybody tell me, why is it happening? What may cause the problem ?
1 answer
Ok, I think I might have solved the problem. The peptide that causes the problem begins with a combination of acids 'ID'. So the command just takes it as a sign that the format of the input is embl. I've changed the call:
needle plain::seq1.txt plain::seq2.txt -datafile EPAM30MS -gapopen 12 -gapextend 2 output
Now it works good.
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Show us the sequence (header + sequence)
I execute the command as shown below:
Each .txt contains only one line that is exactely the sequence. When one of txt presents the sequence 'IDMSAYPVESIR' the troubles begin.
If it is protein sequence you need to add something like
-sprotein1 -sprotein2http://www.bioinformatics.nl/cgi-bin/emboss/help/needleEDIT:
To explain, it is possible that this error did not come up before if the previous "amino acids" are valid IUPAC nucleotides
I've added -sprotein1 -sprotein2 but it didn't get better. So I assume the problem is something else.