CAST 1.2.2 – Compression-accelerated BLAST and BLAT

CAST 1.2.2

:: DESCRIPTION

CAST is a set of tools that compress data in a way that allows direct computation on the compressed data. Compression-accelerated BLAST (CaBLAST) and Compression-accelerated BLAT (CaBLAT) are two prototype implementations of alignment and sequence search algorithms that apply “compressive genomics” : i.e., they exploit redundancy in genomic data sets by compressing data in a way that allows direct computation on the compressed data.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
C++ Compiler
NCBI C++ Toolkit
BLAST+
BLAT

:: DOWNLOAD

CAST

:: MORE INFORMATION

Citation:

Nat Biotechnol. 2012 Jul 10;30(7):627-30. doi: 10.1038/nbt.2241.
Compressive genomics.
Loh PR, Baym M, Berger B.

CaBLASTP 1.0.3 – Performs BLAST on Compressed Proteomic data

CaBLASTP 1.0.3

:: DESCRIPTION

CaBLASTP is a suite of homology search tools, powered by compressively-accelerated protein BLAST, which are significantly faster than and comparably accurate to all known state-of- the-art tools including HHblits, DELTA-BLAST, and PSI-BLAST. Further, our tools are implemented in a manner that allows direct substitution into existing analysis pipelines.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
BLAST+

:: DOWNLOAD

CaBLASTP

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jul 1;29(13):i283-90. doi: 10.1093/bioinformatics/btt214.
Compressive genomics for protein databases.
Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B.

CABRA – Cluster & Annotate Blast Results Algorithm

CABRA

:: DESCRIPTION

CABRA is a web tool , which enables a rapid BLAST search in a variety of updated reference proteomes, and provides a new way to functionally evaluate the results by the subsequent clustering of the hits and annotation of the clusters.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Web Server

:: DOWNLOAD

CABRA

:: MORE INFORMATION

Citation

BMC Res Notes. 2016 Apr 30;9:253. doi: 10.1186/s13104-016-2062-y.
CABRA: Cluster and Annotate Blast Results Algorithm.
Mier P, Andrade-Navarro MA.

ViroBLAST – BLAST web interface

ViroBLAST

:: DESCRIPTION

ViroBLAST is a BLAST web interface for nucleotide and amino acid sequence similarity searches.

ViroBLAST Online Version

::DEVELOPER

Dr. Mullins Labat University of Washington

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/Windows
BLAST

:: DOWNLOAD

ViroBLAST

:: MORE INFORMATION

Citation:

Deng W, Nickle DC, Learn GH, Maust B, and Mullins JI. 2007.
ViroBLAST: A stand-alone BLAST web server for flexible queries of multiple databases and user’s datasets.
Bioinformatics 23(17):2334-2336.

StarPDB – BLAST-based Structural Annotation of a Protein

StarPDB

:: DESCRIPTION

A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures.

::DEVELOPER

StarPDB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BLAST-based structural annotation of protein residues using Protein Data Bank.
Singh H, Raghava GP.
Biol Direct. 2016 Jan 25;11(1):4. doi: 10.1186/s13062-016-0106-9.

BL!P v2.0 – BLAST in Pivot

BL!P v2.0

:: DESCRIPTION

BL!P is a tool that automates NCBI BLAST searches, fetches associated GenBank records, and converts this information into a Silverlight PivotViewer collection. Also, BL!P provides a user interface to create customized images for each BLAST match, allowing the user to further customize their data exploration experience.

::DEVELOPER

Vince Forgetta

:: SCREENSHOTS

:: REQUIREMENTS

Windows
.NET
Microsoft Silverlight

:: DOWNLOAD

BL!P

:: MORE INFORMATION

BEAP 0.6 beta – Blast Extension and Assembly Program

BEAP 0.6 beta

:: DESCRIPTION

The BEAP is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as “primer”, to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the “primer” therefore help to “extend” the length of the original sequence for constructing a “full length” sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis.

::DEVELOPER

NAGRP Bioinformatics Team

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Mac OsX/ WIndows
Perl
Java
NCBI Blast
CAP3

:: DOWNLOAD

BEAP

:: MORE INFORMATION

Citation

James E. Koltes, Zhi-Liang Hu, Eric Fritz and James M. Reecy (2009).
BEAP: The BLAST Extension and Alignment Program — a tool for contig construction and analysis of preliminary genome sequence.
BMC Research Notes 2009, 2:11

CTX-PSI-BLAST 1.0 / CTX-BLAST 1.0 – Context Sensitive version of Protein BLAST

CTX-PSI-BLAST 1.0 / CTX-BLAST 1.0

:: DESCRIPTION

CTX-PSI-BLAST (Contextual PSI-BLAST ) is an extension of NCBI Toolkit that incorporates contextual alignment model into the iterative version of BLAST algorithm known as PSI-BLAST. It allows to investigate the effect of context-dependency in the protein alignment in genomic scale. The software makes use of non-symmetric contextual substitution tables and calculates the statistical significance of a given alignment according to the contextual statistical model.

CTX-BLAST is a software tool that incorporates contextual alignment model into the popular protein BLAST program. Our efficient alignment tool allows us to investigate the effect of context-dependency in the protein alignment in genomic scale. The software makes use of non-symmetric contextual substitution tables and calculates the statistical significance of a given alignment according to the contextual statistical model.

::DEVELOPER

CompBio@MIMUW

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Blast
C++ Complier

:: DOWNLOAD

CTX-PSI-BLAST / CTX-BLAST

:: MORE INFORMATION

Citation:

Bioinformatics. 2007 Jul 1;23(13):1686-8. Epub 2007 Apr 25.
CTX-BLAST: context sensitive version of protein BLAST.
Gambin A, Wojtalewicz P.

FASTA BLAST Scan 2.4 – FASTA & BLAST Alignment Conversion

FASTA BLAST Scan 2.4

:: DESCRIPTION

FASTA BLAST Scan is a program for processing nucleotide sequences alignment made with FASTA and BLAST alignment tools.

::DEVELOPER

Olivier Friard

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

FASTA BLAST Scan

:: MORE INFORMATION

FASTA BLAST Scan is released under the GNU General Public License (GPL)

STORM 1.01 – Protein Analyses of BLAST, FASTA, Pfam and ProtParam

STORM 1.01

:: DESCRIPTION

STORM (Systematic Tailored Orf-data Retrieval & Management) combines protein analyses of BLAST, FASTA, Pfam and ProtParam on a batch-file of protein sequences. It subsequently summarizes and organizes the output in an Access database format.More specifically, STORM extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins. This analysis consists of web-based similarity searches (BLASTp and FASTA) as well as Pfam predictions and Protparam calculations of protein physicochemical properties.

::DEVELOPER

Laboratory of Gene Technology, Katholieke Universiteit Leuven

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Microsoft Access

:: DOWNLOAD

STORM

:: MORE INFORMATION

Citation

Lavigne, R., Sun, W.D. and Volckaert, G.
STORM towards protein function: Systematic Tailored ORF-data Retrieval and Managment.
Applied Bioinformatics (2003) 2(3): 177-179