how i can extract the orthologous sequences

Question

[kamel]

Hi, I used proteinortho on 15 proteomes to extract the orthologue sequences a. I got a matrix prteinortho.txt. could you tell me how i can extract the orthologous sequences between the 15 species to build a phylogeny. Thank you in advance for your help.

# Species   Genes   Alg.-Conn.  Sample1.fasta    Sample2.fasta  Sample3.fasta   Sample4.fasta    Sample 5.fasta Sample6.fasta   Sample7.fasta    Sample8.fasta Sample9.fasta...... Sample 15
15 15   1   FKA_08408-RA     ZKA_09992-RA   FKC_10499-RA    FG005_03202-RA  FKN_11022-RA    FKR_00001-RA    FG851_09649-RA  FKL_12190-RA    FKT_08425-RA

[WouterDeCoster]

(below)

Something is missing.

[kamel]

I forgot to cut the first column of matrix.

[lieven.sterck]

How do you define 'orthologous' ? only 1-to-1 ? also 1-to-many? many-to-many?

[kamel]

according to the manual: the matrix is based on the algebraic connectivity of the respective group. A connectivity of 1 indicates a perfect dense group with each gene similar to each other gene.

[kamel]

Hi h.mon I saw this note in the manual but I did not find an example of use for grap_proteins.pl (is it necessary for example that I give the matrix with the 15 proteomes???,)

[h.mon]

Please use the ADD COMMENT button when commenting on someones answer.

Did you try to run the script without arguments? It should output some help:

./grab_proteins.pl

[Mehmet]

You can also use orthofinder.py tool to get ortholog proteins in your data set. And you will be able to see how many single copy (one-to-one) orthologs are in your dataset. In phylogenetic analyses based on ortholog proteins mostly single copy orthlolog proteins are used.

[kamel]

I will try to use it and come back to you. thank you

Answer 1

[h.mon]

From the manual:

The directory tools contains useful tools, e.g. grab_proteins.pl which fetches protein sequences of orthologous groups from Proteinortho output table