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
•
written
by
diana.leduc
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.
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
Thank you. Diana
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
Log in to answer this question.
