increase local accuracy

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Wei Wang

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Apr 6, 2022, 2:42:55 PMApr 6
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Dear T-COFFEE developers,

I would like to know how to increase local accuracy for a ~10 sequence alignment. For example, here you can see for some 'KVPTY' region, they are not aligned as one would expected. I used '-mode regular'. 

Best regards,

Wei

Screen Shot 2022-04-06 at 14.40.04.png

Wei Wang

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Apr 6, 2022, 3:02:22 PMApr 6
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Another issue is, when I want to use -mode=accurate, I get the error '26054 -- ERROR: BLAST_FAILURE::NCBI does not Support psiblast mode (-j3)'. This is persistent with flag -blast_server EBI or NCBI called. I noticed on GitHub this problem is fixed (https://github.com/cbcrg/tcoffee/issues/39). I do have blast installed via homebrew. Is there anything else I'm missing? thx!

Athanasios Baltzis

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Apr 7, 2022, 7:27:12 AMApr 7
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Dear  Wei,

Can you please share your tcoffee and blast+ versions? I cannot reproduce the issue using T-COFFEE Version_13.45.58.c355d11 and blast+ 2.10.0.

Best,
Athanasios Baltzis
PhD Fellow in Bioinformatics | Data scientist
Notredame's lab - Comparative Bioinformatics Group
Centre for Genomic Regulation (CRG), Barcelona (Spain)

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Wei Wang

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Apr 7, 2022, 10:26:46 AMApr 7
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Thank you! Here they are. 

Screen Shot 2022-04-07 at 10.25.32.png

Athanasios Baltzis

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Apr 7, 2022, 11:54:29 AMApr 7
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I cannot reproduce it using your set-up either. Please try to remove all your tcoffee installations (including the script ncbiblast_lwp.pl) and do a fresh installation of tcoffee. You might need to download the blast+ executables from here https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ .

Best,
Athanasios Baltzis
PhD Fellow in Bioinformatics | Data scientist
Notredame's lab - Comparative Bioinformatics Group
Centre for Genomic Regulation (CRG), Barcelona (Spain)

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