Bug #508
closed
Wrong BLOSUM100 matrix values
Description
Need to replace currently used matrix in:
substitution_matrix.py
With the proper BLOSUM100 matrix, described by NCBI at:
ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM100
Updated by Madeleine Ball almost 16 years ago
A reference we might use for this matrix is:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138974/
Pertsemlidis and Fondon, "Having a BLAST with bioinformatics" Genome Biol. 2001; 2(10): reviews2002.1–reviews2002.10.
Published online 2001 September 27.
The old matrix has 228 of 400 amino acid pairings with a score meeting the threshold of 3 (or 3, after inversion). This new matrix has 240 pairings that meet a threshold of -4, and this set contains all 228 - so, after the matrix is updated to this correct one, the threshold (e.g. used by autoscore) should be changed everywhere.
(A more restrictive threshold of -5 gets 196 pairings, all of which are contained in the set of 228.)
Updated by Madeleine Ball almost 16 years ago
Probably should also change values in the GET-evidence source repository:
/public_html/lib/blosum.php
Updated by Madeleine Ball almost 16 years ago
- Status changed from New to In Progress
Updated by Madeleine Ball almost 16 years ago
New blosum100 added to my GET-evidence branch, thresholds changed. I don't see a need to fix this issue within Trait-o-matic itself (we plan to move those features into GET-E anyway), so this can be considered closed as soon as the master branch is updated.
Updated by Tom Clegg almost 16 years ago
- Status changed from In Progress to Closed
- Resolution set to fixed
Master repo and evidence.personalgenomes.org updated.
Updated by Ward Vandewege about 15 years ago
- Project changed from 19 to GET-Evidence
- Category deleted (
GET-Evidence)