Finding The Common Functions, Processes For Given Proteins

Project Details

Find/list Gene Ontology (GO) annotations (molecular function, biological process and cellular component) and pathways for given proteins

Database : Uniprot
Tools : Python 3.x

##STEPS

• Connect to uniprot.
• Get uniprot access ids of proteins which are given with ensembl and refseq ids
• Use refseq ids and ensembl ids together in the command line
• Get go annotations and pathways of proteins
• Report GO annotations/pathways common to all protein set members.
• Report the frequency of occurrence in the protein set for each GO annotation/pathway

##Usage

• run
  python uniprot_acc_id_finder.py --refseq 'refseq_id'[ --ensembl 'ensembl_id'[ --uniprot--id 'uniprot_id']]

• example command
  python uniprot_acc_id_finder.py --refseq 'NP_000608.1','NP_001139633.1','NP_037305.2'
  or
  python uniprot_acc_id_finder.py --ensembl 'ENSMUSG00000029682' --refseq 'NP_001166492.1' --uniprot_id 'HYALP_MACFA' or
  python uniprot_acc_id_finder.py --refseq 'WP_005082954.1','NP_416893.1','WP_003898649.1' --uniprot_id 'MNTH_BACSU' or
  python uniprot_acc_id_finder.py --ensembl 'ENSMUSG00000023030'

##Requirements

• Internet connection

##Team Members

• [Gizem Abalı] (https://github.com/gizemabali)
• [Ümran İşler] (https://github.com/UmranIsler)
• [Nahide Ergün] (https://github.com/nahidErgun)