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Questions tagged [api]

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1answer
20 views

Getting species from ensembl sequence id

I have downloaded some orthologues from ensembl website in fasta format. The problem is that it uses the ensembl sequence id as name for the sequences. I want to know the species name or any other ...
0
votes
1answer
17 views

How to upload and process a data set to Galaxy instance and retrieve results programmatically?

How to upload and process (de novo assembly pipe) a data set to Galaxy instance and retrieve the results programmatically? Are there any packages beyond BioBlend?
2
votes
0answers
38 views

Number of reactions per metabolic pathway

What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database (kegg, metacyc,reactome..) is more helpful/reliable for ...
5
votes
3answers
132 views

How do you query and explore ENCODE data?

I am looking for a modular way to query data from ENCODE. For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it? Finally, is there an ...
2
votes
1answer
49 views

Error while performing “lift-over” of genomic coordinates between two species using Ensembl Compara API

I'm trying to convert coordinates between the reference mouse genome and CAST/EiJ mice strain. Since Ensebml already has alignment available in the browser, I decided to use Ensembl perl API to lift ...
1
vote
0answers
43 views

Multiple files for case in GDC data portal

I am downloading a set of Copy Number Variation samples from the GDC data API. I noticed that some cases have multiple files (aliquots) for the same case (see for example this case --- here the set of ...
3
votes
1answer
43 views

Automating sequence download from Wormbase

I'm working on the C. elegans model organism, for which there exists an online biological information database: Wormbase. I'm able to manually search for a transcript (say "K06C4.12") and this gets ...
4
votes
2answers
193 views

Retrieve abstract/summary for NCBI bookshelf via Entrez

I want to retrieve abstracts/summaries for NCBI bookshelf entries, eg: "NBK1440" Docs say the dbname is "books" and efetch guide says a rettype of "docsum" works for all databases. However when I ...
4
votes
2answers
756 views

How to map PDB chains to Uniprot IDs using API services

I have a lot of PDB IDs and I need to get uniprot fasta sequences of these PDB IDs special chains by API services. For example, imagine that I need to get fasta sequence of '1kf6' 'A' chain. The ...
12
votes
3answers
972 views

Is there public RESTful api for Gnomad?

I currently find Harvard's RESTful API for ExAC extremely useful and I was hoping that a similar resource is available for Gnomad? Does anyone know of a public access API for Gnomad or possibly any ...
3
votes
2answers
130 views

How can I find mutations associated with disease in human histone residues?

I would like to look if there are mutations in residues of human histones associated with any disease. For instance, if a mutation in residue K6 (lysine 6) of histone H2A1A is associated with any ...
7
votes
2answers
144 views

What methods should I use from PythonCyc API to query metabolites in BioCyc database?

I am using PythonCyc API in order to write a query for metabolites in BioCyc. The purpose of this API is to communicate with the database software of BioCyc- Pathway Tools. Pathway Tools is in lisp ...
11
votes
4answers
359 views

Library for computing BWT-based alignments

I am writing a software tool to which I would like to add the ability to compute alignments using the efficient Burrows-Wheeler Transform (BWT) approach made popular by tools such as BWA and Bowtie. ...