About some tools which can be used to extract domain sequences from several protein sequences

Question

[Ginsea Chen]

Hello everyone

I have about 800 protein sequences which obtained from genome databases, now I want to extract domain parts from these sequences, I don't know whether a software can be used to finish it quickly. If you have some suggestion, tell me please.

Answer 1

[mikhail.shugay]

I could recommend a step that is frequently performed during annotation of de-novo sequenced transcriptomes (http://trinotate.sourceforge.net/). The idea is to utilize HMM-based domain prediction tools such as Pfam/Hmmer (http://hmmer.janelia.org/software). You can also check out InterProScan (http://www.ebi.ac.uk/Tools/pfa/iprscan5/) which performs domain annotations using a huge variety of methods.