:: DESCRIPTION
GenOO is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
GenOO: A programming framework for High Throughput Sequencing analysis
Manolis Maragkakis, Panagiotis Alexiou, Zissimos Mourelatos
doi: https://doi.org/10.1101/019265
:: DESCRIPTION
Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, Bioperl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
An Introduction to BioPerl.
Stajich JE.
Methods Mol Biol. 2007;406:535-48.
:: DESCRIPTION
FASTA Match Regular Expression selects FASTA records whose deflines match a Perl regular expression. Matches can be case-sensitive or case-insensitive.
::DEVELOPER
Statistical Computational Biology Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
FASTA Match Regular Expression
:: MORE INFORMATION
:: DESCRIPTION
mobility is a collection of Perl scripts to calculate gene-level similarity among annotated genomes. The scripts can be executed from the command line and the only dependencies are BioPerl and NCBI BLAST. Separately, we include a MATLAB script to calculate fluidity and its variance directly from matrices of shared and total gene counts.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Kislyuk et al.
Genomic fluidity: an integrative view of gene diversity within microbial populations
BMC Genomics 12: 32 (2011).