Bioinfo tools

From Wiki CEINGE

Jump to: navigation, search

The available tools include the full EMBOSS package, a vast collection of general purpose and more specific sequence handling programs, database search programs, such as FASTA and BLAST, CLUSTALW, programs from the PHYLIP package, a number of programs typically used for protein modelling and RNA structure analysis. Most programs are easily accessible through a Web interface, although command line access remains an option for researchers more familiar with the Unix interface. Fast and prompt execution of the programs is guaranteed by a 112 processor cluster, acting in concert with a number of smaller, multiprocessor servers; program execution is transparently uploaded to the cluster without any specific intervention from the user.

A web application developed within the group, CAPRI, allows access to the programs in a global, collective application which is run on the server, but from the point of view of the user behaves as a typical desktop application, running on each client connected to the system.

About 100 public databases are stored in-house, and the data are kept updated by mirroring: every night updates are downloaded from their primary repositories and integrated with the already available data. Access to the databases is through the SRS interface, also installed and maintained locally by the bioinformatic group (; the SRS installation is one of the most complete in terms of number of databases available and linked tools. The whole ENSEMBL genome browser, complete with all fully sequenced genomes, is also mirrored locally and made available to the users (

Bioinformatics: Bioinfo Services: Bioinfo programs - Databases - Local facilities - Research DB
Personal tools