Search Results for "ncbi blast"
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Showing 22 open source projects for "ncbi blast"
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
...The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software and specific settings can be used to proceed with the taxonomic labeling. TaxOnTree turns its user into an expert on taxonomy. TaxOnTree also corrects for the absence of some taxa in NCBI taxonomy. ... -
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GenTaxo
A perl script for comparative genomics
Requirements: Bioperl NCBI blast+ Usage: perl GenTaxo.pl -ani_files (files separeted by , without space) -aai_files (files separeted by , without space) -evalue (default: 0.001) -threads (default: 1) -verbose (default: False) -min_id (default: 30) -min_cov (default: 0.7) -min_seqs (default: 100) -karlin_files (files separeted by , without space) -output (default: Karlin_Distances.tsv) -verbose (default: False) -
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BlastFilter
Extract good and bad alignments into different files using BLAST+.
BlastFilter uses NCBI BLAST+ to compare sequences to a references. With the threshold set by the user using percentage of identity, the software extract the subject sequences into separate fasta files (good vs bad alignments). -
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simulate_pcr
PCR target prediction software
...It is an open source command line Perl script called simulate_PCR.pl that calls the BLAST (Altschul, et al., 1990) programs makeblastdb, blastn, and blastdbcmd, and the NCBI efetch utility (http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi). -
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reciprocal blast for windows
Pipeline for automatic reciprocal blast
Set of python3 scripts and windows batch scripts which use extensively NCBI Blast+ package and BioPython module to perform algorithm known as reciprocal blast. README: https://sourceforge.net/projects/reciprocalblastwin32/files/ -
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TUIT
Taxonomic Unit Identification Tool
...Read our paper in Biotechniques: http://www.ncbi.nlm.nih.gov/pubmed/24502797 Taxonomic Unit Identification Tool (TUIT) is a free open source platform-independent software, designed specifically to facilitate taxonomic annotation of nucleotide sequences via BLAST homology search against the NCBI databases. TUIT is immediately applicable for both to 16S microboime studies as well as for taxonomic classification of the nucleotide reads. Please see the project's Wiki page. -
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GBLASTN
G-BLASTN is a GPU-accelerated nucleotide alignment tool.
G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. -
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BlastConverter
Converter for NCBI-like BLAST output into XML one.
Different applications (for example Blast2GO) uses BLAST results as a starting point to their analysis. From the other hand, fast BLAST machine allows user to get result very fast. The only problem that can user faced on, that there is no convertor between different BLAST format outputs. Blast2Go requires XML-formatted data while decypher does not producing it. This script is a converter for NCBI-like BLAST output into XML one. -
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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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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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balaBLAST is a free useful tool for the parallel execution of NCBI BLAST. It exploits I/O parallelism and database partitioning, while guaranteeing the same output reporting of a single-core NBCI BLAST. Really easy to install, with package Debian.
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IMAS is a Visual Analytics system for the discovery of knowledge in genomic information. IMAS enables genomic scientists to rapidly analyze and visualize a set of microbial genomic sequences using tools such as Glimmer, Blast, Clustal-W, Primer3.
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JeUtils is an open source program that can be used to automate queries to the National Center for Biotechnology Information (NCBI) using both eUtils and BLAST queries.
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JAMBLAST: Java Application Manager for the ncbi BLAST results. It is a graphic application that allow the user to display, filter, sort, import/export, store/manage BLAST results produced with the NOBLAST (https://sourceforge.net/projects/noblast).
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NoBlast provides a new extended user friendly csv output format and offers an option to correct the statistics when split databases are used for NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn and Tblastx).
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SCAMPI is designed to rapidly detect molecular markers in silico through sequence comparison. For this purpose it creates a unique workflow integrating third party tools like NCBI Blast or Primer3.
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The purpose of Mitrion-C Open Bio Project is to develop FPGA accelerated bioinformatics applications for the Mitrion Virtual Processor. The first accelerated application is NCBI BLAST.
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FSA-BLAST is a new version of the popular BLAST (Basic Local Alignment Search Tool) bioinformatics tool, used to search genomic databases containing either protein or nucleotide sequences. FSA-BLAST is twice as fast as NCBI-BLAST with no loss in accuracy.
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WinBlast is a Windows graphical front-end for NCBI BLAST. It is written completely in C#, utilizing Microsofts latest .NET framework. WinBlast will run on any Windows machine that supports Microsoft .NET framework.
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A bi-directional BLAST tool for orthologue listing with extended facilities (global alignment; paralogue list; GO onthology; dN/dS; etc) working on Win32 compiled versions of NCBI BLAST,FASTA,EMBOSS, and PAML. FILES AVAILABLE AT THE HOMEPAGE.(JAVA coded)
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