IbrahimTanyalcin / MutaFrame

Bug Reports / Feature Requests / API documentation for MutaFrame

MutaFrame is a single page web app that makes diease predictions on Human Proteome accessible.

Services

We provide client side ui at mutaframe.com and also several other APIs with proper Access-Control-Allow-Origin: * headers . When you use our apis, your base uri is always https://deogen2.mutaframe.com/. You need to make a [GET] request to the appropriate path to receive a response.

General rate limiting rules apply, you can make up to ~45 calls per minute, which after you'll start receiving 403. After a minute, you should be good to go again.

tools/pseudo?query=

You can search for a gene symbol, accession or a phrase enclosed between quotes, you receive a json response of the information available.

Query Parameters

field	desc	default	required
query	alpha numeric	NA	required
species	common name or taxonomy id	human	optional
isoforms	retrieve all isoforms	false	optional
refseq	retrieve only refseq	false	optional

Return Value

Array

Examples

GET https://deogen2.mutaframe.com/tools/pseudo?query="breast cancer 2" 

[{"mrna":"NM_000059.4","protein":"NP_000050.3","uniprot":"P51587","name":"BRCA2 DNA repair associated","symbol":"BRCA2"}]

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GET https://deogen2.mutaframe.com/tools/pseudo?query=TUBA1A&isoforms=true

[{"mrna":"NM_001270399.1","protein":"NP_001257328.1","uniprot":"Q71U36","name":"tubulin alpha 1a","symbol":"TUBA1A"},{"mrna":"NM_001270400.1","protein":"NP_001257329.1","uniprot":"Q71U36","name":"tubulin alpha 1a","symbol":"TUBA1A"},{"mrna":"NM_006009.4","protein":"NP_006000.2","uniprot":"Q71U36","name":"tubulin alpha 1a","symbol":"TUBA1A"}]

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GET https://deogen2.mutaframe.com/tools/pseudo?query=NM_001130916.2&refseq=true

[{"mrna":"NM_004612.4","protein":"NP_004603.1","uniprot":"P36897","name":"transforming growth factor beta receptor 1","symbol":"TGFBR1"}]
 

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tools/seqfetch?accession=

Provide an accession number and receive back the sequences if the latest refseq version exists.

Query Parameters

field	desc	default	required
accession	entrez accession	NA	required
fields	protein,mRNA	NA	required
response	return format	json	optional
download	trigger download	false	optional
refseq	only refseq	false	optional

Return Value

Object

Examples

GET https://deogen2.mutaframe.com/tools/seqfetch?accession=NM_001130916.2&fields=mrna,protein&response=json

//{"protein":"MEAAVAAP...","mrna":"aaagggccggagcga..."}

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GET https://deogen2.mutaframe.com/tools/seqfetch?accession=NM_001130916.2&fields=protein&response=json

//{"protein":"MEAAVAAP..."}

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GET https://deogen2.mutaframe.com/tools/seqfetch?accession=NM_001130916.2&fields=protein&response=fasta

//> NM_001130916.2 protein
MEAAVAAPRPRLL...

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You can trigger a browser side download as well:

GET https://deogen2.mutaframe.com/tools/seqfetch?accession=NM_001130916.2&fields=protein&response=json&download=true

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tools/orf

ORF (Open Reading Frame) is a sequence finder that relies on "pseudo" and "seqfetch" services. If you want to use the automated retrieved leave the mrna or protein section empty and type your keyword into the other.

Alternatively you can copy paste mrna and protein sequences on their respective lines and click "ANALYZE" to check if the given protein sequence is found within one of the six possible frames of the given mrna.

[ Try ORF ]

You can add as many sequences as you like, they will be justified to the left for comparison:

tools/scorefetch

Query Parameters

field	desc	default	required
uniprot_accession	uniprot accession	NA	required
interval	interval	1,sequence.length	optional
fields	return fields	NA	required

Return Value

Array. Empty object if bad request is received

Examples

GET https://deogen2.mutaframe.com/tools/scorefetch?uniprot_accession=P19838&fields=pr,ci&interval=1,11-20,30-40

[{"name":"M1A","pr":"-0.806","ci":"0.1102190986535408"},{"name":"M1C","pr":"-1.169","ci":"0.1102190986535408"},{"name":"M1D","pr":"-1.563","ci":"0.1102190986535408"},{"name":"M1E","pr":"-1.274","ci":"0.1102190986535408"},{"name":"M1F","pr":"-0.995",....

[ Try it ]

Status

You can track site and API status at https://status.mutaframe.com/

Bug reports and issues related to MutaFrame

• Describe the issue in a few sentences
• If applicable, write down the UniprotID, if the bug appears in a specific protein
• Provide a screenshot of your console, by right clicking on an empty area and selecting "Inspect".
• Specify if the bug only appears on a certain browser or reproducible accross the board

Feature request

• Describe the feature you'd like it to be added in a few sentences.
• Provide a link or a simple drawing which depicts feature if possible

Performance issues

• If you have suggestions for performance increase, take a screen shot of the area where the affected element is located
• If you have performance issues, describe the issue in a few sentences. If possible provide your rig's specs.
• If applicable, specifiy if the performance issue is present across all browsers, or confined to a specific one.

Supporting

You can support Mutaframe by:

• following at
• creating an account at MutaFrame
• helping us create better software by submitting bug reports or feature requests