Help with finding gene families in genome

Question

[Elizabeth]

Hi all, I'm looking for tools/sites/softwares/codes that can help me identify gene families such as GPCR or NHR in my newly sequenced eukaryotic genome. The genome size is around 60Mb. Thanks.

[lieven.sterck]

Is your question related to constructing gene families or more towards functionally annotation gene families?

[Elizabeth]

Functional annotation of gene families

[Mehmet]

If you have a gene file (amino acid sequences) from your genome and you want to know which gene families your genes belong to,

You can use:

1. Pfam website; (you need to split your gene file into small files)

http://pfam.xfam.org/search#tabview=tab1

1. you can use hmmer that also uses Pfam database. (You do not need to split).

http://hmmer.org

Answer 1

[lieven.sterck]

Depending on your species, you can have a look at this one as well : Trapid

Alternatively you can do interproscan searches (somewhat in line with Mehmet's answer) and especially have a look at the superfamily and Panther output (they specifically denote 'gene families' )

These will still only get you info on a gene by gene basis, so you still will have to extrapolate that to the gene fams you have.

[Elizabeth]

Thank you everyone. I am using B2go software package for functional annotation. I am looking for Glyceraldehyde-3-phosphate dehydrogenase (GPD) gene family. During the blast run, I get a hit on two contigs that codes for the GPD gene, but interproscan does not return any hit. So, can I include these hits in the GPD family category ?

Answer 2

[Rohit]

Omicstools is a good source for suggestions. If you have the amino acid sequences, interproscan does a great job in annotation. If you are looking into TMM or signal peptides in particular, signalP or TMHMM are useful. Trinotate is another annotation pipeline setup for de novo stuff.