<p>BLAST is often a sensible way to find gene/protein homologs, but resolving those as orthologs vs paralogs etc. is a non-trivial task, especially when considering large numbers of species.</p>

<p>Since you are new to bioinformatics I recommend you search an ortholog database that already exists.</p>

<p>Here are some databases:</p>

<ul>
<li><a href="https://www.orthodb.org/" rel="noreferrer">orthoDB</a>  </li>
<li><a href="https://omabrowser.org/oma/home/" rel="noreferrer">OMA</a>  </li>
<li><a href="http://eggnogdb.embl.de/#/app/home" rel="noreferrer">EggNog</a></li>
</ul>

<p>All of these should allow you to search either with text or a sequence to identify the orthologous groups that your input belongs to at different taxonomic levels. Sequence searches either follow pairwise alignment (e.g. BLAST, DIAMOND, RAPSEARCH) or profile HMM type (e.g. HMMER3) approaches.</p>

<p>A more complete list of ortholog databases is available from "<a href="https://questfororthologs.org/orthology_databases" rel="noreferrer">Quest for orthologs</a>".</p>

CC BY-SA 4.0
2018-11-21T17:02:28.520Z
2018-11-22T08:18:01.193Z
2018-11-22T08:18:01.193Z
Chris_Rands
<p>Two solutions based around the same premise:</p>

<ol>
<li><p>Repeat the blast using "blastp". I suspect you have used blastn (nucleotides). To translate the gene Expasy is okay and find the common "translate", <a href="https://web.expasy.org/translate/" rel="nofollow noreferrer">here</a>.</p></li>
<li><p>Blasted via Blastx without any modification to the gene.</p></li>
</ol>

<p>Blast is capable of doing just about anything if you are aware of all its parameters. </p>

<p>The reasoning is that the gene you have will be under-represented in the database. By switching to amino acids there is a much greater chance of finding orthologous hits. </p>

CC BY-SA 4.0
2018-12-16T03:38:05.830Z
2018-12-16T03:38:05.830Z
M__
<p>Without jumping deep into the rabbit hole of orthologology, you can just use <a href="http://www.ensembl.org/biomart/martview/" rel="nofollow noreferrer">biomart</a></p>

<p>An instruction is <a href="http://www.ensembl.info/2009/01/21/how-to-get-all-the-orthologous-genes-between-two-species/" rel="nofollow noreferrer">here</a> </p>

CC BY-SA 4.0
2020-06-17T15:24:25.543Z
2020-06-17T15:24:25.543Z
Code42
<p>I'm an informatics student who has essentially zero knowledge of biology. I BLASTed my gene and have 1000s of results with very low E values. Where do I go from here if I want to find orthologues?</p>

CC BY-SA 4.0
2018-11-21T17:28:01.183Z
Please [edit] your question and give us some more details. What type of blast? Blastn? Tblastn? Blastx? Something else? Is your database protein or nucleotide? And your query? What species are you working with? What kind of orthologs do you want? (see [here](https://biology.stackexchange.com/q/4962/1306) for a short discussion of orthologs vs paralogs; I suspect you just want general homologs).
terdon
<blast><orthologues>
Finding orthologues using BLAST on the NCBI database
# Finding orthologues using BLAST on the NCBI database

(Asked by: username_0 on 2018-11-21)

I'm an informatics student who has essentially zero knowledge of biology. I BLASTed my gene and have 1000s of results with very low E values. Where do I go from here if I want to find orthologues?

**Tags:** blast, orthologues
> **Comments:**
> **username_1**: Please [edit] your question and give us some more details. What type of blast? Blastn? Tblastn? Blastx? Something else? Is your database protein or nucleotide? And your query? What species are you working with? What kind of orthologs do you want? (see [here](https://biology.stackexchange.com/q/4962/1306) for a short discussion of orthologs vs paralogs; I suspect you just want general homologs).  

---

## 3 answers

### Answer by username_2 on 2018-11-21. Score: 7

BLAST is often a sensible way to find gene/protein homologs, but resolving those as orthologs vs paralogs etc. is a non-trivial task, especially when considering large numbers of species.

Since you are new to bioinformatics I recommend you search an ortholog database that already exists.

Here are some databases:

* [orthoDB](https://www.orthodb.org/)
* [OMA](https://omabrowser.org/oma/home/)
* [EggNog](http://eggnogdb.embl.de/#/app/home)

All of these should allow you to search either with text or a sequence to identify the orthologous groups that your input belongs to at different taxonomic levels. Sequence searches either follow pairwise alignment (e.g. BLAST, DIAMOND, RAPSEARCH) or profile HMM type (e.g. HMMER3) approaches.

A more complete list of ortholog databases is available from "[Quest for orthologs](https://questfororthologs.org/orthology_databases)".


---

### Answer by username_3 on 2018-12-16. Score: 0

Two solutions based around the same premise:

1. Repeat the blast using "blastp". I suspect you have used blastn (nucleotides). To translate the gene Expasy is okay and find the common "translate", [here](https://web.expasy.org/translate/).
2. Blasted via Blastx without any modification to the gene.

Blast is capable of doing just about anything if you are aware of all its parameters.

The reasoning is that the gene you have will be under-represented in the database. By switching to amino acids there is a much greater chance of finding orthologous hits.


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### Answer by username_4 on 2020-06-17. Score: 0

Without jumping deep into the rabbit hole of orthologology, you can just use [biomart](http://www.ensembl.org/biomart/martview/)

An instruction is [here](http://www.ensembl.info/2009/01/21/how-to-get-all-the-orthologous-genes-between-two-species/)


---

