Search Results for "blast" - Page 3
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Showing 113 open source projects for "blast"
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blastplot
A simple and easy to use perl package to plot blast output results
...We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. BLASTPLOT is a simple to use PERL module that allows the generation of PNG graphs for all the reference sequences associated with a BLAST result set. BLASTPLOT has only two PERL package dependencies: Math::Round and GD. -
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Cylindrical BLAST Viewer
Alignments in Rotating Cylinder / 3D
3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App -
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CodaChrome
CodaChrome: The Pan-Genomic Explorer
CodaChrome is a tool for visually exploring how the proteome of a bacterium of interest relates to every other finished bacterial genome in GenBank. -
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Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
OrthoRBH is a tool/pipeline designed to identify families of protein coding transcripts/genes in related species using a reciprocal blast method. It can search through databases of full-length cDNAs, ESTs or mRNA-seq data. Optional assembly of candidate sequences allows assembly of contigs. It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs sequence alignment and deposits sequences into a fasta sequence file for downstream molecular evolutionary analysis. -
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MatrixMaker
Custom substitution matrix creator
Create custom substitution matrices for BLAST protein search. Easy to use GUI based application. -
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...The web server and standalone version of Geptop are available at http://cefg.uestc.edu.cn/geptop/ free of charge. This package is dependent on Python, Biopython and BLAST+. Citation: Wei W, Ning L-W, Ye Y-N, Guo F-B (2013) Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny. PLoS ONE 8(8): e72343. doi:10.1371/journal.pone.0072343
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Precipice
PC / console game where you play as an Undead deity taking over earth
Game Features: 1) Play as the Undead Prince Of Darkness! Hack, slash, shoot, and blast your way through the human's reign and take over cities one-by-one. Protect your investments by positioning "Nodes" that allow for health and spell regeneration 2) Raise the dead! Control armies of Undead "Minions", lead them into battle, and raise them from human corpses via your "Grave-Robber" spell. The dead will literally rise from graves and dead bodies to assist you in battle. -
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ProGraphMSA
Graph-based multiple sequence alignment
...This is achieved by incorporating a graph-based sequence representation as in POA and combines it with the advantages of the phylogeny-aware algorithm in Prank. Further, we account for variations in the substitution pattern by using estimated amino acid frequencies and by implementing context-specific profiles as in CS-Blast. The latest versions of ProGraphMSA include and extension to the alignment model to support tandem repeat unit insertions and deletions. -
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GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.
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SkyRiotFree
SkyRiot Free For Android
...Fly a hoverboard and use an assortment of weaponry as you, an anarchist, single-handedly wage war against a totalitarian regime. Full 360-degree aiming along with total freedom of movement will keep you glued to your device for many hours as you blast your way across over 10 game maps. The fascist regime will squash your airborne rebellion with laser equipped police officers, bazooka toting soldiers, law enforcing surveillance orbs, jet fighter airplanes, grenade throwing prison guards, even a jetpack powered security force. -
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Files included are the programs De-MetaST and De-MetaST-BLAST. Additional screencast tutorial videos are provided to describe how to install these programs as well as examples for executing both De-MetaST and De-MetaST-BLAST. ++++++++++++++++++++++++++++ De-MetaST = metagenome search tool -output: FASTA file of retrieved amplicons -tutorial video: install_De-MetaST.mp4 De-MetaST-BLAST = metagenome search tool + BLAST -output: (1)FASTA file of retrieved amplicons and (2)TXT file of predicted functions for each amplicon -tutorial videos: (1)install_local_BLAST.mp4 and (2)install_De-MetaST-BLAST.mp4 ++++++++++++++++++++++++++++ All files must first be uncompressed before use. ...
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birgHPCC
Rapid CUDA Cluster Deployment
...In addition to the increase in image size (less than 2 gigabytes) and a new Linux base (previously Debian, now Ubuntu), CUDA-capable bioinformatics software programs, such as NAMD, HOOMD-blue, VMD, GPU-HMMER and GPU-BLAST, are pre-installed in birgHPCC, along with the CUDA driver, libraries and software development kit (SDK). In short, birgHPCC is the world's first CUDA-ready, bioinformatics-based, live DVD. -
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A ready-to-use Python application program run in Windows operating system to BLAST query and re-BLAST returned hits for protein sequence verification.
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brocc
BLAST Read and OTU Consensus Classifier
NOW HOSTED ON GITHUB: https://github.com/kylebittinger/brocc Old releases are kept here for archival purposes. -
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TBIS
Total Business Information System (TBIS)
Scope : Combination of CRM+ERP+Score Card/KPI Database : MySQL + Oracle Language : PHP Platform : Linux/Unix/Windows mail me at shukrijasin[at]gmail.com if you want to access the demo account for TBIS NEW new purchasing system :- PURCHA demo link :- http://sga-systems.com/purcha login :- oop/123 hamsani/123 (admin) -
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The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.
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metaProt
Pipeline to analyze coding regions in metagenomic projects
metaProt is a python pipeline to analyze and extract data from protein sequences found in metagenomic projects. It integrates several existing tools (HMMer, Pepstats, Blast...) to be used against custom databases. Please, read the README.txt file to find more about this. -
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Mass Blaster
Dual Ship Shoot'em Up Game
Mass Blaster is one of the most intense arcade shooters for Windows and Linux. You will take control of two ships simultaneously to blast away at the invading Square Army. On your left, take down enemies with the red n' rad Trigerus. On your right, command the cool blue Pythagora to wipe out your foes. Choose from 4 modes of difficulty to fight your way through 10 gutsy levels. Only those with the skills to pilot both ships at the same time will go on to become High Score Heroes. -
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TBARMapper
Finds mutations of M. tuberculosis
It maps sequencing reads with MTB reference genome (H37Rv) using NCBI blast, and finds out mutation sites. -
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BioX (pronounce as bio cross) is a system for the management of local and remote (currently supporting RMI, CORBA and SOAP Web Services) components such as files and services (e.g. BLAST). Additionally, the components can be composed to workflows.
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Signal And Noise Estimation Procedure Including Correlation (SANEPIC) has been originaly developped by G. Patanchon to be used on data from the Ballon-borne Large Aperture Submillimeter Telescope experiment (BLAST) . It has been modularized and generalized to other bolometer array by A. Beelen & M. Husson. SANEPIC has been applied with success to LABOCA and Herschel-SPIRE data.
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MultiArtemis imports BLAST output (with -m 8 specified) into Artemis genome browser (www.sanger.ac.uk) entries. It is designed for mapping multiple contigs or scaffolds back to reference sequence and view.
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NumericalFISH is a bioinformatics graphical tool for easy analysis of BLAST or BLAT results, especially aimed at the study of duplications or segmental duplications.
