Tcoffee and "Segment-based multiple sequence alignment"

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Ibrahim Chegrane

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Nov 20, 2020, 3:44:15 PM11/20/20

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Hello,

I am ibrahim chegrane, postdoctoral researcher at bio-informatics lab in Sherbrooke University (Quebec).

I am very interested by tcoffee; and the paper "Segment-based multiple sequence alignment, by Tobias Rausch et al."(https://academic.oup.com/bioinformatics/article/24/16/i187/200409))

My question: is the algorithm of Tobias Rausch is part of (or implemented in) Tcoffee. If yes how we can use it.

In The abstract of the paper we read:

Availability:The segment-based multiple sequence alignment toolcan be downloaded from http://www.seqan.de/projects/msa.html. A novel version of T-Coffee interfaced with the tool is available fromhttp://www.tcoffee.org. The usage of the tool is described in both documentations

We searched in the documentation of T-Coffee, but we didn't succeed to find if the Algorithm is implemented or not, and how we use it.

In the tcoffee read the doc, we can find the reference for Tobias paper here : https://tcoffee.readthedocs.io/en/latest/tcoffee_citations_references.html?highlight=Rausch#comparative-genomics-biology

But, we can't find where it is cited.

In The web page of "t-coffee-lib-format-01": https://tcoffee.readthedocs.io/en/latest/tcoffee_technical_documentation.html#t-coffee-lib-format-01

There is the possibility to declare ranges of residues rather than single pairs (+BLOCK+ 10 12 14 99), so we suspect that mean that maybe t-coffee will use directly the segment based algorithm hence Tobias paper. Is it true, or it has nothing to do with it.

Another point, I didn't really understand the (+BLOCK+...), t-coffe will consider the whole segment, or it will consider each residues in the block? which mean that +BLOCK+ is only a compressed write of multiple line of succicifive single residues.

Thank you very much for helping me 🙂

Ibrahim Chegrane

CoBIUS lab.

https://cobius.usherbrooke.ca/

CoBIUS Lab – Computational Biology

CoBIUS: We are a Computational Biology Team at the Computer Science (Informatique) Department of Université de Sherbrooke with team members from diverse backgrounds and origins bringing various expertises.The lab is headed by Professor Aïda Ouangraoua, Ph.D., MSc Eng, and we work in close collaboration with life scientists to validate our tools by solving biological questions on real data.