[phenixbb] FASTA format for sequence file

Randy Read rjr27 at cam.ac.uk
Tue Feb 6 00:13:01 PST 2018


I have some recollection that we may have made the error report more informative, if you're using an older version.

Here, off the top of my head, are some possibilities for what is wrong:

1. The sequence contains a letter other than the 20 representing standard amino acids.

2. When you say "carrot", you mean "caret", i.e. the character "^", or something else other than the greater-than sign ">" that is used to identify the line with the name.

3. Something that looks like a normal allowed letter is actually a similar-looking special symbol.

When other people have had similar problems, it has sometimes been due to saving a sequence as RTF or Word format, but I think you've ruled out that possibility with your tests.  On a Unix system, you can make sure by giving a command like "file mysequence.seq" and checking that it returns "ASCII text".

If none of those possibilities cover what is happening, could you send me examples of the sequence files that are and are not accepted by Phaser?


Best wishes,

Randy Read

> On 5 Feb 2018, at 23:54, egoers at uoregon.edu wrote:
> Hello,
> I'm trying to run Phase-MR on Phenix (older version) and having trouble formatting my sequence properly. I keep getting error "Protein Sequence not recognized in Composition". I have a good idea of what FASTA should look like (carrot with a name, no spaces or weird characters, followed by the sequence in all capital letter on the next line). I have tried many things, mainly using gedit and plain text files (.txt). I've made sure the file name doesn't have any strange characters as well. If I cut and paste a FASTA file from the PDB into gedit, save that at a .txt, Phaser accepts it. If I cut and paste my protein sequence into the same file, it rejects it. Suggestions?
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Randy J. Read
Department of Haematology, University of Cambridge
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