TCS scoring results not consistent between local and web TCS - gaps management - T-coffee 13.41.139.ca96b3d

[AlbanMariette]

Hello,
I am currently using t-coffee to perform multiple sequence alignment of proteins to study evolution of transmembrane protein.
I started using the web-hosted t-coffee system, however as I plan to analyse a large number of sequence (1000) I am now using a locally-installed t-coffee (T-COFFEE Version_13.41.139.ca96b3d (2020-07-23 15:47:56 - Revision 7788a2c - Build 604).
I am currently aligning ~140 proteins for a test and I am unsuccessful at using TCS on this PSI/TM-coffeee alignment.

When I use the TCS web server on this set of protein ( T-COFFEE Version_11.00.d625267 (2016-01-11 15:25:41 - Revision d625267 - Build 507) I get a proper scoring of each residue however when I use the local version (see above) the scoring doesn't seem to work because I almost only get 0 for the residues (same alignment fed to the system).
I am using the following command (which seems to be the same of the one used on the web-hosted t-coffee):
t_coffee -infile result.fasta_aln -in Mproba_pair -score 1 -output score_ascii aln tcs_replicate_100 score_html tcs_column_filter3 tcs_column_filter2 tcs_column_filter1

I ran a test on three transmembrane proteins, I aligned them using t-coffee and then scored the alignment using the webhosted TCS and my local TCS. I obtained the same results on the two systems, however the alignment of these three proteins contain less gaps that my 140 proteins alignment. I suspect that there is something different with the management of the gaps in the scoring system between the two different version of the software.

Could you help me figure out what is happening ?
Thanks for your time. If you need more information please let me know !
Alban

[cnotred]

Dear Alban Thanks you for the feedback. We have done quite some work on psi coffee and it may be that there is an issue Can I ask you, in this order, to double check with the latest beta and, if the problem persists to send me your dataset Best regards Cedric ################################### Dr Cedric Notredame Group Leader Notredame's lab - Comparative Bioinformatics Group Bioinformatics and Genomics Programme Room 440.03 Centre de Regulació Genòmica (CRG) Dr. Aiguader, 88 08003 Barcelona Spain Ph# + 34 93 316 02 71 Fax# + 34 93 316 00 99 Mobile# + 34 66 250 47 82 email [email protected] url www.tcoffee.org blog cedricnotredame.blogspot.com ORC-ID: 0000-0003-1461-0988 ###################################

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On 14 Sep 2020, at 03:11, Alban MARIETTE ***@***.***> wrote:  Hello, I am currently using t-coffee to perform multiple sequence alignment of proteins to study evolution of transmembrane protein. I started using the web-hosted t-coffee system, however as I plan to analyse a large number of sequence (1000) I am now using a locally-installed t-coffee (T-COFFEE Version_13.41.139.ca96b3d (2020-07-23 15:47:56 - Revision 7788a2c - Build 604). I am currently aligning ~140 proteins for a test and I am unsuccessful at using TCS on this PSI/TM-coffeee alignment. When I use the TCS web server on this set of protein ( T-COFFEE Version_11.00.d625267 (2016-01-11 15:25:41 - Revision d625267 - Build 507) I get a proper scoring of each residue however when I use the local version (see above) the scoring doesn't seem to work because I almost only get 0 for the residues (same alignment fed to the system). I am using the following command (which seems to be the same of the one used on the web-hosted t-coffee): t_coffee -infile result.fasta_aln -in Mproba_pair -score 1 -output score_ascii aln tcs_replicate_100 score_html tcs_column_filter3 tcs_column_filter2 tcs_column_filter1 I ran a test on three transmembrane proteins, I aligned them using t-coffee and then scored the alignment using the webhosted TCS and my local TCS. I obtained the same results on the two systems, however the alignment of these three proteins contain less gaps that my 140 proteins alignment. I suspect that there is something different with the management of the gaps in the scoring system between the two different version of the software. Could you help me figure out what is happening ? Thanks for your time. If you need more information please let me know ! Alban — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[AlbanMariette]

Dear Cedric,
Thanks for your quick reply, I will contact the admin of the HPC I am using and run a test on the beta ASAP.
I will keep you updated.
Best regards,
Alban