Question: Help with finding gene families in genome
0
gravatar for Elizabeth
2.6 years ago by
Elizabeth20
Elizabeth20 wrote:

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.

gene family • 855 views
ADD COMMENTlink modified 2.6 years ago by Rohit1.4k • written 2.6 years ago by Elizabeth20

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

ADD REPLYlink written 2.6 years ago by lieven.sterck8.9k

Functional annotation of gene families

ADD REPLYlink written 2.6 years ago by Elizabeth20

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

ADD REPLYlink written 2.6 years ago by Mehmet630
0
gravatar for lieven.sterck
2.6 years ago by
lieven.sterck8.9k
VIB, Ghent, Belgium
lieven.sterck8.9k wrote:

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.

ADD COMMENTlink written 2.6 years ago by lieven.sterck8.9k

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 ?

ADD REPLYlink written 2.6 years ago by Elizabeth20
0
gravatar for Rohit
2.6 years ago by
Rohit1.4k
California
Rohit1.4k wrote:

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.

ADD COMMENTlink written 2.6 years ago by Rohit1.4k
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