This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how to annotate transcriptome

hello everyone!
i have a transcriptome which include around 144777 sequences. i want to annotate this sequences to know what protein there are represented for with the latest protein database? could anyone tell me how can i do that? if i can, can i do that work by my laptop( with intel(R) core (TM)i5-3200M CPU @ 2.60GHz (4 CPU),~26 GHz; 4G RAM, 500G hard driver)? if i can , how ?

please give me some suggestions!!

annotation
• 4,814 views • link
updated by Ram Ram • written by Kurban Kurban

Thank you @pcsam

I did as you suggested for practise by using cloudblast via blastx, and that will really help me. But how many sequences can I annotate at once at most? Because my fasta file contain about 140000 sequences, should I divide them to several file for blast?

• 0 views • link
updated by Ram Ram • written by Kurban Kurban

it doesn't need any division, i think blast2GO can work on your file.

• 0 views • link
written by Whoknows Whoknows

hello @pcsam

thank you. if u look at my location u might understand. at the bigining blast2go did not work at all, then i changed my proxy it starts to work ,but very slow. so if i vivided the file teen parts i can finish it teen days.

anyway, thank you , i learned a lot

• 0 views • link
written by Kurban Kurban

1 answer

You can use Blast2GO tool, it takes sequences and align them with NCBI non-redundant (nr) database proteins and gives you result.

Download blast2go java version and load your sequence file then just blast it via Blastx, it so easy.

• 0 views • link
written by Whoknows Whoknows

Log in to answer this question.

More posts like this