On Fri, Nov 19, 2010 at 10:27 AM, Bryan Lepore <span dir="ltr"><<a href="mailto:bryanlepore@gmail.com">bryanlepore@gmail.com</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
trouble with alignment format. tried this :<br>
<br>
fubar.fas :<br>
Sorry: Unknown file(s): fubar.fas<br>
<br>
fubar.fasta :<br>
Sorry: Wrong alignment format: fubar.fasta<br>
<br>
i compared to one that worked yesterday and its not obvious : first<br>
sequence is the target, the pdb sequence is in there (somewhere), i<br>
changed a ">sp" to ">gi"....<br></blockquote><div><br></div><div>The extension ".fas" is not recognized, but ".fasta" should be. �My experience with the FASTA parser (for simple sequences, at least) is that it's extremely strict about what is an acceptable format, but that most of the programs/servers that generate/distribute these files are much looser. �Could you send me the file (off-list, of course) for debugging?</div>
<div><br></div><div>-Nat</div></div>