Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014)

SeqDepot

Frequently Asked Questions


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» Which browsers work with SeqDepot?

Because all access to the SeqDepot database uses the REST API interface, any program capable of RESTful requests is compatible. This includes all modern web browsers.

Google Chrome Mozilla Firefox Safari Internet Explorer Opera

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» How do I know if SeqDepot contains my sequence?

Send a GET request to:

http://seqdepot.net/api/v1/aseqs/{aseq-id}

Where {aseq-id} is the Aseq ID representing your sequence and check the HTTP status code. SeqDepot contains the sequence if the HTTP status code is 200.

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» What is a GET (or POST) request?

A GET request is simply an HTTP network request made using the HTTP GET method. Each time you submit a URL into the address bar of your web browser, you are making a GET request to that resource.

POST requests are similar to GET requests except that they use the HTTP POST method and may carry additional data in the body of the request. This most commonly occurs when submitting forms on the web. Both GET and POST along with others are standard parts of the HTTP protocol for Internet communication.

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» What is an Aseq ID?

An Aseq ID is a 22 character identifier derived solely from an amino acid sequence and is unique to that exact sequence. Any two sequences that are 100% identical will have identical Aseq IDs. Because Aseq IDs are derived directly from the sequence itself, they have two very desirable traits. Namely, they are immutable (and thus perfectly stable) and database agnostic. Aseq ID's are purely related to their intrinsic sequence characters and not dependent on any external database.

See: How are Aseq ID's derived from a sequence?

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» What sequence databases are used to populate SeqDepot?

The amino acid sequences in SeqDepot are regularly imported from two major sources:

  1. SIMAP: The Similarity Matrix of Proteins. The SIMAP project specializes in the distributed precomputation of sequence similarity between all known proteins. SIMAP's primary sequence source is InterPro, which aggregates several major sequence databases (GenBank, European Nucleotide Archive, DDBJ, UniProt, PDB, and others). Additionally, SIMAP spans metagenomic data sets including the human microbiome.
  2. MiST: Microbial Signal Transduction Database