Gblocks file not opened error

Question

[sa.youssef]

I am trying to extract the conserved regions from the MSA file but when I open the file, it is stated file not opened even that was in a FASTA format, and I have tried to convert it to PIR, and didn't work as well. Any suggestions, please?

[Mensur Dlakic]

As always:

• a sample (first 5-10 lines) of your MSA file
• what was the command you used?
• what was the exact error message?
• what program did you use for PIR conversion and what was the error message?

Shouldn't some abbreviated guidelines like this be shown at the top of each "New Post" form?

Answer 1

[brian.fristensky]

The following will process a FASTA protein file called seqs.fsa at the command line:

Gblocks seqs.fsa -t=p

It will create two files: seqs.fsa-gb (a FASTA file with the selected positions) and seqs.fsa-gb.htm (an HTML report showing the selected positions). The -t parameter would be "d" for DNA.

Gblocks can be run as a point-and-click function in the BIRCH system. An example can be seen in the BIRCH phylogeny tutorial Distance methods.