Multiple Sequence Alignments by Theodor Sperlea

Author:Theodor Sperlea
Language: eng
Format: epub
ISBN: 9783662644737
Publisher: Springer Berlin Heidelberg

3.2.23 PSI-Coffee and TM-Coffee

PSI-Coffee and TM-Coffee are two very similar functioning programs of the T-Coffee family. Both use homology extension as a first step to generate the T-Coffee typical libraries [27, 50].

For this purpose, the sequences to be aligned are used as queries for PSI-BLAST searches. The results of the searches that show a sequence identity of 50 - 90% and an overlap of >70% with the respective source sequence are then combined with the latter to form a sequence profile. These sequence profiles show how evolutionarily variable the individual sites of the sequences to be aligned are. The library, from which the MSA is finally calculated, is obtained from PSAs generated on the basis of a pair HMM.

While for PSI-Coffee a database of non-redundant protein sequences from UniProt with >50% sequence identity is searched with PSI-BLAST, in the case of TM-Coffee the database consists exclusively of transmembrane domains, giving it high accuracy for MSAs for transmembrane proteins [15].

Download

Copyright Disclaimer:
This site does not store any files on its server. We only index and link to content provided by other sites. Please contact the content providers to delete copyright contents if any and email us, we'll remove relevant links or contents immediately.