Treefam To Asign Gene Families

Question

[diana.leduc]

I have got about 1000 de novo predicted genes and would like to assign them to families using the TreeFam Database. On http://www.treefam.org/ you can search the database by entering the protein sequence. Is there any way to upload a file with the sequences and retrieve the homologs and the gene family assigned for each of these?

Thanks in advance for any input,

Diana

Answer 1

[arnstrm]

You can actually download all the HMM profiles of treefam and use them to scan your proteins. You can either use HMMER or their own treefam_scan script. The latter has extensive documentation and is easier to use, I guess.

If you are not comfortable using command-line/unix, then you can try OrthoMCL. But unlike TreeFam, it is BLAST based.

[diana.leduc]

Hi,

Thanks a lot for the answer. So I would need to follow the steps here https://github.com/treefam/treefam_tools/tree/master/treefam_scan, if I understand it correctly. Do I have to have API Ensembl installed for that? My best,

Diana

[arnstrm]

yes, links in the scripts requires api's to be installed.

[diana.leduc]

Thank you. Diana

[diana.leduc]

One more question. What cutoffs are usually set for asigning the family? Alignment length and e value. And also, how are the single copy orthologous families defined? Thank you for the help.

Diana