Question: Archieve of homologous nucleotide sequence across genome
gravatar for CY
26 days ago by
United States
CY370 wrote:

I am looking for any reference file that archieves homologous nucleotide sequence (homologous gene) across genome. It could a file harbored in FTP site, a database or a tool for that. Does anyone have any recommendation?

P.S. For clarification, what I would like to get is a list of genes or regions (in human genome) that have similar (homologous) sequences (in human genome). For example, gene ABC1, ABC2 and ABC3 (assuming these are ABC homologs and share similar nucleotide sequence). It would be preferable if I can get a list like this directly. Alternatively, I can use tools such as biopython BLAST E-util or ClustalW to make such list. However, this is a new field to me and I have no idea how should I proceed.

sequence • 116 views
ADD COMMENTlink modified 20 days ago by juanjo75es60 • written 26 days ago by CY370

NCBI Homologene, UCSC multi-genome comparisons (example for human, others available, look in pairwise and multiple alignments) and Ensembl Compara.

ADD REPLYlink modified 26 days ago • written 26 days ago by genomax71k
gravatar for h.mon
26 days ago by
h.mon27k wrote:

OrthoDB and OMA Orthology Database, among others, have the information you want.

ADD COMMENTlink written 26 days ago by h.mon27k

Sorry for confusion. What I meant is to get the homologous genes / regions across human genome.

ADD REPLYlink written 26 days ago by CY370

You could start by looking for paralogs. You can find them in Ensembl using the compara API or BioMart.

ADD REPLYlink written 26 days ago by Jean-Karim Heriche20k
gravatar for juanjo75es
20 days ago by
juanjo75es60 wrote:

Apart from BLAST you can now try that link. It makes use of a different technology and looks for homolog matches with the same length instead of submatches as BLAST does.

ADD COMMENTlink written 20 days ago by juanjo75es60
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