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Conserved regions of an alignment

Hello,

Is there any tool that I can find conserved regions of an alignment and create a list with them?

alignment protein sequence
• 2,835 views • link
updated by h.mon h.mon • written by l.souza l.souza

1 answer

Maybe trimAl can do what you need. Latest version download on GitHub.

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written by h.mon h.mon

Correct me if I'm wrong, but trimAl removes the non-conserved regions and makes a new sequence with the conserved regions. I'd like to have a list with the conserved regions (and informations like their coordinates, window size, etc) inside the alignment.

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written by l.souza l.souza

Maybe these options?

   -sgc        Print gap percentage count for columns in the input alignment.
   -scc        Print conservation values for columns in the input alignment.
   -sident     Print identity statistics for all sequences in the alignemnt. (see User Guide).
• 0 views • link
written by h.mon h.mon

These options doesn't show me neither the coordinates nor the window size!

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written by l.souza l.souza

See some perl code here, you can modify it to match your needs.

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written by h.mon h.mon

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