seqdepot.net

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SeqDepot | seqdepot.net Reviews

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Source agnostic, non-redundant, biological sequence repository

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Source agnostic, non-redundant, biological sequence repository

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SeqDepot

http://www.seqdepot.net/api

Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). Many database projects consist of at least two major layers: 1) the underlying database itself and 2) a custom front end with very specific views of the database contents. These views typically decorate the raw data within an HTML page for presentation purposes. Often this is the only publicly accessible representation of the data. For example, the MiST. While this works to varying degrees, " screen scraping. Suffers from several problems. REST: the wa...

2

SeqDepot

http://www.seqdepot.net/stats

Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). 8,934,788,107. Transmembrane regions ( DAS. Low complexity regions (seg). Signal peptides ( SignalP. Subcellular locations ( TargetP. Transmembrane regions ( TMHMM. Developed and maintained by Luke Ulrich.

3

SeqDepot

http://www.seqdepot.net/faq

Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). Which browsers work with SeqDepot? How do I know if SeqDepot contains my sequence? What is a GET (or POST) request? How do I use the REST API? What is an Aseq ID? What sequence databases are used to populate SeqDepot? Raquo; 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. Send a GET request. An Aseq I...

4

SeqDepot

http://www.seqdepot.net/docs

Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). SeqDepot was borne out of a. Need to easily and rapidly access precomputed data. For protein sequences. Moreover, it is computationally wasteful to repeatedly analyze identical sequences that yield the same results. Many useful resources with similar goals already exist, so why build another one? Inability to add new sequences. We need to incorporate novel sequences on demand to support downstream projects (processing new genomes into MiST. At its core...

5

SeqDepot

http://www.seqdepot.net/query

Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). TSV: Aseq ID (Base64 MD5). TSV: MD5 hex IDs. Request / Response details. One result per line, tab-delimited [query, http response code, aseqId,. Data, user data]). MSMDISDFYQTFFDEADELLADMEQHLLVLQPEAPDAEQLNAIFRAAHSIKGGAGTFGFS VLQETTHLMENLLDEARRGEMQLNTDIINLFLETKDIMQEQLDAYKQSQEPDAASFDYIC QALRQLALEAKGETPSAVTRLSVVAKSEPQDEQSRSQSPRRIILSRLKAGEVDLLEEELG HLTTLTDVVKGADSLSAILPGDIAEDDITAVLCFVIEADQITFETVEVSPKISTPPVLKL AAEQAPTGRVEREKTTRSNESTSIRVAVEKVDQLINLVGELVITQSML...

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Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). 2 Dec 2014: Domain architecture images (PNG and SVG) are now drawn by using pfam27 hits. 10 Oct 2014: SeqDepot is updated with non-redundant database. SeqDepot massively simplifies the retrieval of primary sequences and associated secondary data by:. Consolidating protein sequences and precomputed data. Via a well-documented REST API. Supplying tools to rapidly integrate knowledge of interest. By minimizing the data retrieval. SeqDepot can benefit anyo...

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