<p>Apparently there is a <a href="https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/FASTA+Help+and+Documentation#FASTAHelpandDocumentation-RESTAPI" rel="nofollow noreferrer">REST API for FASTA</a>. Looks like there are few dependencies but other than that should be straightforward to use.</p>

CC BY-SA 4.0
2022-02-18T19:50:36.147Z
2022-02-18T19:50:36.147Z
haci
<p>I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command line actually) which has a similar output to the FASTA tool, i.e:</p>
<p><a href="https://i.sstatic.net/hgDzZ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/hgDzZ.png" alt="enter image description here" /></a></p>
<p>For my use case, the 'Source' column is not super relevant, so it does not matter if it's not included in the output. What's most important is the DB:ID and the match statistics.</p>
<p>Have you used anything similar? Do you have any suggestions regarding such a tool?
Thanks in advance!</p>

CC BY-SA 4.0
2022-02-18T21:13:14.213Z
Hmmm ... two suggestions, you can do both via Python, Blast or a tree matrix. Its an interesting question but difficult to know what you're looking for
M__
CC BY-SA 4.0
2022-02-20T12:28:21.833Z
Will you be comparing specific, known sequences, or is part of the question finding similar sequences to your query in a large database of non-related sequences? Basicaly, do you want a sequence aligner (mafft, t_coffee, clustal etc) or tools like the various flavors of blast (psi-blast, p-blast)? Or are you looking for proteins with shared domains which means tools like HMMER or psi-blast again? Pretty much everything in bioinformatics can be done from the command line, so you need to explain exactly what question you're trying to answer for us to suggest the better options.
terdon
<phylogenetics><fasta><python><proteins>
Programmatic way of accessing the FASTA sequence similarity tool (or similar) in Python
# Programmatic way of accessing the FASTA sequence similarity tool (or similar) in Python

(Asked by: username_0 on 2022-02-18)

I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command line actually) which has a similar output to the FASTA tool, i.e:

[![enter image description here](https://i.sstatic.net/hgDzZ.png)](https://i.sstatic.net/hgDzZ.png)

For my use case, the 'Source' column is not super relevant, so it does not matter if it's not included in the output. What's most important is the DB:ID and the match statistics.

Have you used anything similar? Do you have any suggestions regarding such a tool?
Thanks in advance!

**Tags:** phylogenetics, fasta, python, proteins
> **Comments:**
> **username_1**: Hmmm ... two suggestions, you can do both via Python, Blast or a tree matrix. Its an interesting question but difficult to know what you're looking for  
> **username_2**: Will you be comparing specific, known sequences, or is part of the question finding similar sequences to your query in a large database of non-related sequences? Basicaly, do you want a sequence aligner (mafft, t_coffee, clustal etc) or tools like the various flavors of blast (psi-blast, p-blast)? Or are you looking for proteins with shared domains which means tools like HMMER or psi-blast again? Pretty much everything in bioinformatics can be done from the command line, so you need to explain exactly what question you're trying to answer for us to suggest the better options.  

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## 1 answers

### Answer by username_3 on 2022-02-18. Score: 2 | Accepted answer

Apparently there is a [REST API for FASTA](https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/FASTA+Help+and+Documentation#FASTAHelpandDocumentation-RESTAPI). Looks like there are few dependencies but other than that should be straightforward to use.


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