Rationale
You're a bioinformatics researcher. You've got a list of proteins that you're interested in. You want to find out which of these proteins have been localised to the cytosol. You also want to find out which of these have mass spec data. For that matter, you'd like to know where the experimental phosphorylation sites are. You can script that all up with this.
You've got a sequence dataset with a bunch of annotations on it. You'd like to visualise the annotation on the proteins. You want to be able to publish this online somewhere easily. You can do all that with this.
Features
- Command-line interface using nodejs
- Local caching of data in-browser or on-disk
- Ability to rate-limit calls to web-services
- Internet Explorer 9+ support
- Mobile safari support
Services and data available
| Data type | Services | Class |
|---|---|---|
| Localisation | SUBA | MASCP.SubaReader
|
| Mass spectrometric | pep2pro | MASCP.AtProteomeReader
|
| PPDB | MASCP.PpdbReader
| |
| ProMEX | MASCP.PromexReader
| |
| AtPeptide | MASCP.AtPeptideReader
| |
| AT_CHLORO | MASCP.AtChloroReader
| |
| At GelMap | MASCP.GelMapReader
| |
| Phosphorylation | PhosPhAt | MASCP.PhosphatReader
|
| RIPP-DB | MASCP.RippdbReader
| |
| P3DB | MASCP.P3dbReader
| |
| nsSNP | SNP data | MASCP.SnpReader
|
Who?
beleaguered bioinformagician
Working on ways to write decent code while getting decent publications out of the door.
Get it
Download the Latest release, or visit the project page at GitHub.
Availability of documentation
Right now, official documentation is sparse. If anyone wishes to pitch in writing the documentation, please get in contact with me.
Sandbox
To do simple API calls, you can use the following sandbox.
- find_sequence(agi)
- res = get_data(agi,SERVICE)
- res = find_peptide(agi,peptide)
- res = find_motif(agi,/regexp/)
- res = find_region(agi,[start,end])