Projects

ProDy

ProDy is a free and open-source Python package for analysis and modeling of protein structural dynamics. It allows for efficient analysis of large datasets and is suitable for development or prototyping of structure-based analysis and modeling software.

SequenceServer

A simple web front end to NCBI BLAST+ that lets users share, and consume sequence data intuitively. "The iPod of Blast searching" Set up your local BLAST server in minutes...

mono-biosharp

Actually bioinformatics needs new tools that provides complete and valid information faster and easy.to extract sequences from genbank or another data sources. to process sequences and to fill databases. to represent sequences in a human readable user interface. your request. You will needMono ... [More] Runtime >= 1.9 Tool GenBank2AnyGenBank2Any allows to cut a GenBank file the output could be html ,text or pdf format files. each html, text or pdf generated file contains a complete sequence data Download tool here: GenBank2Any0.2.tar.gz [Less]

furnace

Furnace is a grid-enabled version of NCBI BLAST. Furnace takes files in FASTA format, splits them into sequences of configurable length, and submits them to a grid for processing. Each grid node runs the sequence against an instance of NCBI BLAST.

jjv

jjv is an open source gene finding application designed to annotate prokaryote genomes. It uses a two phase search; the first is a "content-based" search designed to find candidate genes and the second is a "similarity-based" search, using a known genome to compare the candidate ... [More] genes with and to judge the probability that they are indeed genes. [Less]

panic-at-home

The main idea of PANIC@Home, based on the program Blast, distribute the workload thought the web in a easy way. Using java clients to pick sequences from a server, compare and put the result in the server again. Without Globus, MPI, PVM, nothing! Just a Java client, and a LAMP or WAMP server. =)

blastomim

For clinical genomics works.

sequencing

This project sequences a give set of DNA sequences against Arabidopsis CDS file in TAIR database. It is useful if you want to know how good is your PCR results. The inputs are

biogui

GUI for highly used command-line bioinformatics tools such as BLAST, BLAST Parser.Currently, I am rewriting all the modules. You can read the the news on the BioGUI blog (on the right of your screen) for the development. The following GUIs are available: GUI Seq: A GUI for biological sequence ... [More] transformation. GUI Blast: A GUI for running NCBI BLAST. GUI Blast Parser: A GUI for parsing BLAST output. Note: biogui_windows_full.rar is packaged for Windows users, while biogui_linux_full.tar.bz2 is packaged for Linux users. USAGE: Windows: Untar biogui_windows_full.rar, Double click biogui.py. Linux: Untar biogui_linux_full.tar.bz2, python biogui.py [Less]

mpiblast-build

mpiblast is a powerful tool for searching dna sequences. This project seeks to provide a simplified and unified interface to install recent versions of ncbi toolkit and the mpiblast primary sources.