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

 NO

:: 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.

BLAST / netBlast 2.9.0 – Find Regions of Similarity between Sequences

BLAST / net Blast 2.9.0

:: DESCRIPTION

BLAST (Basic Local Alignment Search Tool) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

netblast (network-client BLAST) can search all the sequences in a FASTA file, produce one-to-many (master-slave) alignments in text or HTML format. It can also perform searches against multiple databases.

::DEVELOPER

NCBI

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Mac OsX / Windows

:: DOWNLOAD

BLAST / netBlast

:: MORE INFORMATION

BLAST is public domain software.

Citation:

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) “Basic local alignment search tool.” J. Mol. Biol. 215:403-410. PubMed

More……

BlasterJS – JavaScript based BLAST Alignments Viewer

BlasterJS

:: DESCRIPTION

BlasterJS is a free to use, open source JavaScript based BLAST alignments viewer, with support for both single and multiple alignments.

::DEVELOPER

SING Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 BlasterJS

:: MORE INFORMATION

BDBM 0.17.0 – BLAST DataBase Manager

BDBM 0.17.0

:: DESCRIPTION

BDBM provides a graphical user interface that allows you to create high quality sequence datasets using the tools included. Using these tools you can perform several common tasks such as doing BLAST alignments, getting the open reading frames of the sequences in a Fasta file or changing the format of a Fasta file.

::DEVELOPER

The SING research group

:: SCREENSHOTS

BDBM

:: REQUIREMENTS

  • Mac OsX / Linux
  • Java
  • EMBOSS
  • bedtools
  • NCBI’s BLAST

:: DOWNLOAD

 BDBM

:: MORE INFORMATION

SequenceServer 1.0.6 – Set up a Local BLAST Web Server to Search & Share Sequence data

SequenceServer 1.0.6

:: DESCRIPTION

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

::DEVELOPER

Wurm Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SequenceServer

:: MORE INFORMATION

Citation

Sequenceserver: a modern graphical user interface for custom BLAST databases
Anurag Priyam, Ben J Woodcroft, Vivek Rai, Alekhya Munagala, Ismail Moghul, Filip Ter, Mark Anthony Gibbins, HongKee Moon, Guy Leonard, Wolfgang Rumpf, Yannick Wurm
doi: http://dx.doi.org/10.1101/033142

CAST 1.2.1 – Compression-accelerated BLAST and BLAT

CAST 1.2.1

:: 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.

BLASTO – BLAST on Orthologous groups

BLASTO

:: DESCRIPTION

BLASTO is a modified BLAST tool for searching orthologous group data. BLASTO treats each ortholog group as a unit, and instead of providing a ranked list of individual sequence hits, it organizes and ranks the BLAST results by ortholog groups, which is often a much more desirable format for functional inference or evolutionary studies.

::DEVELOPER

The Landweber Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W678-82. Epub 2007 May 5.
BLASTO: a tool for searching orthologous groups.
Zhou Y, Landweber LF.