AlignIO #47

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tiagoantao opened this Issue Apr 22, 2016 · 2 comments

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@tiagoantao
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I have tried to clean AlignIO but it needs some (minor) love from a module specialist:

  • the PFAM database is no more
  • one bugzilla reference
@lennax
Contributor
lennax commented Apr 22, 2016

The bug link is here: https://redmine.open-bio.org/issues/2557

PFAM has moved here: http://pfam.xfam.org/
But the linked alignment is "dead": http://pfam.xfam.org/family/PF09395
And the new family is http://pfam.xfam.org/family/PF08702
The seed alignment now has 75 sequences. I'd recommend switching to RP15 because it only has 17 sequences.

I also noticed there is a rendered backslash in PF09395\_seed.sth (in the paragraph right above the alignment example code).

@peterjc peterjc added a commit that referenced this issue Apr 29, 2016
@peterjc peterjc Update bug URL (bugzilla --> redmine)
Thank you @lennax, noted on #47
f0a0ad8
@peterjc
Member
peterjc commented Apr 29, 2016

I've fixed some of this, but @lennax is right - the example I choose could be replaced with something smaller like RP15.

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