dali_sp – Script for DaliLite to perform Serial Structure Comparison

dali_sp

:: DESCRIPTION

dali_sp is a wrapper script for DaliLite to perform serial structure comparison and to merge output pairwise alignments into single multiple alignment.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 dali_sp

:: MORE INFORMATION

PSI-BLAST-ISS 1.04 – The PSI-BLAST Intermediate Sequence Search tool

PSI-BLAST-ISS 1.04

:: DESCRIPTION

PSI-BLAST-ISS is a standalone Unix-based tool designed to delineate reliable regions of sequence alignments as well as to suggest potential variants in unreliable regions. The region-specific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of alignment variants. The PSI-BLAST-ISS output enables the user to simultaneously analyze alignment reliability between query and multiple homologous sequences. In addition, PSI-BLAST-ISS can be used to detect distantly related homologous proteins.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 PSI-BLAST-ISS

:: MORE INFORMATION

Citation

Margelevicius M., Venclovas C. (2005)
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability.
BMC Bioinformatics 6(1):185

Re-searcher 1.4 – System for Recurrent Searches of Homologs in Protein Sequence databases

Re-searcher 1.4

:: DESCRIPTION

Re-searcher is a user-friendly configurable system for recurrent searches and reporting of new homologs in specified protein sequence databases. Searches can be performed at desired intervals either within NCBI or local databases using BLAST or PSI-BLAST. In addition to searches against an individual database, the system can perform “PDB-BLAST”-like combined searches, when PSI-BLAST profile generated during search against the first database is used to search the second database. The system supports multiple users each keeping track of multiple queries and query-specific results.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

Researcher

::REQUIREMENTS

  • Windows/Linux
  • Web Server
  • Java

:: DOWNLOAD

  Re-searcher

:: MORE INFORMATION

Citation

Repšys V., Margelevičius M. and Venclovas Č. (2008)
Re-searcher: a system for recurrent detection of homologous protein sequences.
BMC Bioinformatics 2008, 9:296

COMA 1.10 – Detection of Distant Evolutionary Relationships

COMA 1.10

:: DESCRIPTION

COMA (Comparison Of Multiple Alignments) is a method for detection of distant evolutionary relationship (homology) through comparison of multiple protein sequence alignments. For convenience, the COMA software package includes programs for constructing profiles from multiple alignments, generating a profile database from a set of profiles, searching a profile (multiple alignment) against a profile database, etc. COMA output consists of pairwise alignments between profiles (multiple alignments) with estimated values of statistical significance, which indicates the probability that the aligned pair of profiles is a random match.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 COMA

:: MORE INFORMATION

Citation

Margelevičius M., Venclovas Č. (2010)
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparisons.
BMC Bioinformatics, 2010 11:89.

TRIC – Alignment Tool for Targeted Proteomics

TRIC

:: DESCRIPTION

TRIC is an alignment software for targeted proteomics (SRM or SWATH-MS) data. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate information from all available runs. The input consists of a set of csv files derived from a targeted proteomics experiment generated by OpenSWATH (using either mProphet or pyProphet) or generated by Peakview.

::DEVELOPER

Aebersold Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TRIC

:: MORE INFORMATION

Citation

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.
Röst HL, Liu Y, D’Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R.
Nat Methods. 2016 Aug 1. doi: 10.1038/nmeth.3954.

sBWT 1.0b1 – Burrows–Wheeler transform (BWT) based Fast Indexer/Aligner

sBWT 1.0b1

:: DESCRIPTION

sBWT is a Burrows–Wheeler transform (BWT) based fast indexer/aligner specialized in parallelized indexing and searching for Next Generation Sequencing data.

::DEVELOPER

sBWT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 sBWT

:: MORE INFORMATION

Citation

sBWT: Memory Efficient Implementation of the Hardware-acceleration-friendly Schindler Transform for the Fast Biological Sequence Mapping.
Chang CH, Chou MT, Wu YC, Hong TW, Li YL, Yang CH, Hung JH.
Bioinformatics. 2016 Jul 13. pii: btw419.

MSAViewer 1.0.0 – Multiple Sequence Alignment Viewer

MSAViewer 1.0.0

:: DESCRIPTION

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size.

::DEVELOPER

MSAViewer team

:: SCREENSHOTS

MSAViewer

:: REQUIREMENTS

  • JavaScript

:: DOWNLOAD

 MSAViewer

:: MORE INFORMATION

Citation

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.
Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis S, Rost B, Goldberg T.
Bioinformatics. 2016 Jul 13. pii: btw474.

MAFFT 7.299 – Multiple Alignment Program

MAFFT 7.299

:: DESCRIPTION

MAFFT (Multiple sequence Alignment based on Fast Fourier Transform)is a multiple sequence alignment program for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~10,000 sequences), etc.

MAFFT Server

::DEVELOPER

Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp> and Hiroyuki Toh

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/ Linux

:: DOWNLOAD

MAFFT

:: MORE INFORMATION

Citation

Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees.
Yamada KD, Tomii K, Katoh K.
Bioinformatics. 2016 Jul 4. pii: btw412

Kazutaka Katoh and Hiroyuki Toh
Parallelization of the MAFFT multiple sequence alignment program
Bioinformatics (2010) 26 (15): 1899-1900

SMAL – Scaffold-Based Multiple Network Aligner

SMAL

:: DESCRIPTION

The SMAL web-server is a public, open-source, web-based application for creating multiple network alignments (MNAs) from existing pairwise alignments (PNAs).

::DEVELOPER

Biocomputing and Media Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

The SMAL web server: global multiple network alignment from pairwise alignments.
Dohrmann J, Singh R.
Bioinformatics. 2016 Jul 4. pii: btw402.

deBGA – de Bruijn Graph-based Aligner

deBGA

:: DESCRIPTION

deBGA is a seed-and-extension-based read alignment tool. It is suitable for aligning various kinds of high-throughput sequencing reads to multiple similar reference genomes.

::DEVELOPER

HIT Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 deBGA

:: MORE INFORMATION

Citation:

deBGA: read alignment with de Bruijn Graph-based seed and extension.
Liu B, Guo H, Brudno M, Wang Y.
Bioinformatics. 2016 Jul 4. pii: btw371.