Automatic bibliography from Blast output
This project has developed during my postgrade degree specialising in Bioinformatics (DESS Bioinformatique) at Lille University.
The Project
The goal of this project is to obtain articles references of relative sequences to a given GENBANK id. The application was supposed to retrieve the author's name and the abstract for the found articles from MEDLINE or PUBMED.
Project parts
The project is composed of a script in PERL Language. The script takes in parameter a GENBANK ID, then launch a BLAST search. Then, for all results with a E-value lower than a given threshold , it retrieves title and abstract of all relative PubMed articles without redondancy.
For this project, I used the LWP (libwww-perl) module. I used the NCBI website, for BLAST requests and for articles search in the PubMed and MedLine database. In addition, the script supports connection throughout a proxy server.
Project files
Project files are available here(tar archive).
Project demonstration
Example:
biblio.pl AAC72193 0.01
The Blast result output page(missing)
The obtained PubMed result page (missing)
Contact the author: 