1.Brief Introduction

We provide programmatic access to various data resources and analysis tools via our web service APIs. To ensure client and server software from various sources will work well together, the web services are built on the REpresentational State Transfer (REST) open standard.

2.How to use?

The following steps will guide you how to use the web services.

Step 1: Download a client program in the section3 form.

Step 2: Configure the client-side environment. Java,Perl or Python and libraries of dependencies are required.You can use pip to install Python packages and cpan to search and install Perl modules.

Step 3: Run the client program. Firstly, run the program without any arguments to see details of usage, then submit your job with proper arguments. The following are two examples of job submission using the Python2 clients:


  python psisearch2d_urllib2.py --email <email> --database <db> --sequence <seqFile> --evalue 0.001 --num_iter 3 [options...]


  python wesCromwellcommon_urlib2.py -S <sampleid> --email <email> --title <title> --adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --qc_quality 20 --uploadid <uploadid>

Note: For WGS and WES, please use the Upload Tool provided at the bottom of the table underneath. You will get a UploadID from the Upload Tool and process WGS/WES analysis with the UploadID .

3.Web Service Clients

Sample clients are provided for multiple programming languages. For details of how to use these clients, download the client and run the program without any arguments.
Tools Description Language Download Requirements
PSISearch2D PSISearch2D Query-seeded sequence iterative search with novel visualizations for domain & sequence alignments ,combined with Simth-Warterman algorithm. Perl psisearch2d_lwp.pl LWP and XML::Simple
Python2 psisearch2d_urllib2.py urllib2 and xmltramp
Python3 psisearch2d_urllib3.py urllib3 and xmltramp2
Java psisearch2d.jar Java 8
SBT BLAST SBT-BLAST combined SBT algorithm and BLAST to perform ultrafast local alignment search in large scale RNA-seq data. Perl sbtblast_lwp.pl LWP and XML::Simple
Python2 sbtblast_urllib2.py urllib2 and xmltramp
Python3 sbtblast_urllib3.py urllib3 and xmltramp2
Java sbtblast.jar Java 8
BLAST BLAST stands for Basic Local Alignment Search Tool.The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of your sequence. Perl ncbiblast_lwp.pl LWP and XML::Simple
Python2 ncbiblast_urllib2.py urllib2 and xmltramp
Python3 ncbiblast_urllib3.py urllib3 and xmltramp2
Java ncbiblast.jar Java 8
FASTA FASTA (pronounced FAST-AYE) is a suite of programs for searching nucleotide or protein databases with a query sequence. FASTA itself performs a local heuristic search of a protein or nucleotide database for a query of the same type. FASTX and FASTY translate a nucleotide query for searching a protein database. TFASTX and TFASTY translate a nucleotide database to be searched with a protein query. Optimal searches are available with the programs SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query against local database). Perl fasta_lwp.pl LWP and XML::Simple
Python2 fasta_urllib2.py urllib2 and xmltramp
Python3 fasta_urllib3.py urllib3 and xmltramp2
Java fasta.jar Java 8
Clustal-Omega Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms. Perl clustalo_lwp.pl LWP and XML::Simple
Python2 clustalo_urllib_python27.py urllib2 and xmltramp
Python3 clustalo_urllib3.py urllib3 and xmltramp2
Java clustalo.jar Java 8
InterProScan5 InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem. Perl iprscan5_lwp.pl LWP and XML::Simple
Python2 iprscan5_urllib2.py urllib2 and xmltramp
Python3 iprscan5_urllib3.py urllib3 and xmltramp2
Java iprscan5.jar Java 8
DeepSea Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Perl deepsea.pl LWP and XML::Simple
Python2 deepsea_urllib2.py urllib2 and xmltramp
Python3 deepsea_urllib3.py urllib3 and xmltramp2
Java deepsea.jar java8
Sequence Profiler Sequence Profiler is a ultility of DeepSEA that performs "in silico saturated mutagenesis" analysis for discovering informative sequence features. Perl deepsea2_lwp.pl LWP and XML::Simple
Python2 deepsea2_urllib2.py urllib2 and xmltramp
Python3 deepsea2_urllib3.py urllib3 and xmltramp2
Java SequenceProfiler.jar java8
DeepBind Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Perl deepbind.pl LWP and XML::Simple
Python2 deepbind_urllib2.py urllib2 and xmltramp
Python3 deepbind_urllib3.py urllib3 and xmltramp2
Java deepbind.jar java8
WES Human Whole Exome Sequencing Analysis Workflow(Cromwell implement) Perl wesCromwellcommon.pl LWP and XML::Simple
Python2 wesCromwellcommon_urllib2.py urllib2 , xmltramp and json
Python3 wesCromwellcommon_urllib3.py urllib3 , xmltramp2 and json
Java wescromwell.jar java8
WESMAKE Human Whole Exome Sequencing Analysis Workflow(make implement) Perl wesMakecommon.pl LWP and XML::Simple
Python2 wesMakecommon_urllib2.py urllib2 , xmltramp and json
Python3 wesMakecommon_urllib3.py urllib3 , xmltramp2 and json
Java wesMake.jar java8
WGS Human Whole Genome Sequencing Analysis Workflow Perl wgscommon.pl LWP and XML::Simple
Python2 wgscommon_urllib2.py urllib2 , xmltramp and json
Python3 wgscommon_urllib3.py urllib3 , xmltramp2 and json
Java wgs.jar java8
Upload Tool Upload Tool provides data upload service for our WGS/WES workflow analysis. Python2 wgscommon_urllib2.py requests
Python3 wgscommon_urllib2.py requests