Tag: Alignment / BLAST

NetAligner 1.0 – Fast and Accurate Alignment of Protein Interaction Networks

NetAligner 1.0

:: DESCRIPTION

NetAligner is a novel network alignment tool that allows the identification of conserved protein complexes and pathways across organisms, providing valuable hints as to how those interaction networks evolved.

::DEVELOPER

Structural Bioinformatics and Network Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Winodows / Linux / MacOsX

:: DOWNLOAD

NetAligner

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W157-61. doi: 10.1093/nar/gks446. Epub 2012 May 22.
NetAligner–a network alignment server to compare complexes, pathways and whole interactomes.
Pache RA1, Céol A, Aloy P.

SnS-Align – Alignment of Distantly related Proteins

SnS-Align

:: DESCRIPTION

SnS-Align (Structure and Sequence Alignment) is a tool developed in perl, used to align the protein sequences by combining sequence and structure information at an instance. Given a protein sequence of an organism, the tool is used to identify its homologue(s) in the evolutionarily distant organisms, which might not be found from either sequence alone or structure alone comparisons.

::DEVELOPER

Rakesh Mishra Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SnS-Align

:: MORE INFORMATION

Citation:

Ganiraju Manyam, Ancha Baranova, Mikhail Skoblov and Rakesh K. Mishra.
SnS-Align: A graphic tool for alignment of distantly related proteins.
International Journal of Bioinformatics Research & Applications (IJBRA) 5, 663-673, 2009.

ProSplign 20170203 – Alignment of Proteins against Genomic Sequences

ProSplign 20170203

:: DESCRIPTION

ProSplign is a global alignment tool developed by Dr. Boris Kiryutin. It produces accurate spliced alignments and locates alignments of distantly related proteins with low similarity.

::DEVELOPER

Dr. Boris Kiryutin (kiryutin@ncbi.nlm.nih.gov)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ProSplign

:: MORE INFORMATION

Citation

ProSplign – Protein to Genomic Alignment Tool.
B. Kiryutin, A. Souvorov, T. Tatusova.
Manuscript in preparation

JAligner 1.0 – Biological Local Pairwise Sequence Alignment

JAligner 1.0

:: DESCRIPTION

JAligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh’s improvement for biological local pairwise sequence alignment using the affine gap penalty model.

::DEVELOPER

Ahmed Moustafa 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 JAligner

:: MORE INFORMATION

BLAT 36 – Rapid mRNA/DNA & Cross-species Protein Alignments

BLAT 36

:: DESCRIPTION

BLAT (BLAST -like alignment tool) is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.

BLAT Online Version

::DEVELOPER

Jim Kent

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 BLAT ; Source Code

:: MORE INFORMATION

Citation

Kent, W.J. 2002.
BLAT — The BLAST-Like Alignment Tool.
Genome Research 4: 656-664

Squint 1.02 – Multiple Sequence Alignment Editor

Squint 1.02

:: DESCRIPTION

Squint is an advanced alignment tool. It brings together algorithmic alignment of molecular sequences, with human editing. It is an extension of the alignment editor available in Pebble.

::DEVELOPER

the New Zealand Bioinformatics Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 Squint

:: MORE INFORMATION

Citation:

Goode, M. and Rodrigo, A. G., (2007),
SQUINT: A multiple alignment program and editor.,
Bioinformatics 23:1553-1555.

PALES – Prediction of ALignmEnt from Structure

PALES

:: DESCRIPTION

PALES is a software for analysis of residual dipolar couplings. Its main component is the PALES (Prediction of ALignmEnt from Structure) simulation that predicts the magnitude and orientation of a sterically induced alignment tensor from a solute’s (protein/nucleic acid/oligosaccharide) three-dimensional shape.

::DEVELOPER

Research Group Zweckstetter

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX/ Windows

:: DOWNLOAD

 PALES

:: MORE INFORMATION

Citation

NMR: prediction of molecular alignment from structure using the PALES software.
Zweckstetter M.
Nat Protoc. 2008;3(4):679-90. doi: 10.1038/nprot.2008.36.

SimAssemblyStage1/2 0.2 – Assembly Alignment of Contigs

SimAssemblyStage1/2 0.2

:: DESCRIPTION

SimAssemblyStage1: Perfectly aligns TranscriptSimulator reads to their nucleotide templates using read title inforamation, creating ideal simulated assembly of super contigs.

SimAssemblyStage2: Creates an optimal simulated assembly alignment of contigs using the output of SimAssemblyStage1.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SimAssemblyStage1/2

:: MORE INFORMATION

Chromaligner – Chromatogram Alignment

Chromaligner

:: DESCRIPTION

Chromaligner is a tool for chromatogram alignment. It could be used for chromatograms generated by various chromatographic methods such as high performance liquid chromatography and capillary electrophoresis. Time shift is a frequent encountered problem in gradient elution or capillary electrophoresis. Chromaligner used a constrained chromatogram alignment method to resolve this issue.

::DEVELOPER

Chromaligner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2338-9. doi: 10.1093/bioinformatics/btq337. Epub 2010 Jun 23.
Chromaligner: a web server for chromatogram alignment.
Wang SY1, Ho TJ, Kuo CH, Tseng YJ.

DIAlignR v1.1.2 – Chromatogram Alignment for Targeted Proteomics

DIAlignR v1.1.2

:: DESCRIPTION

DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.

::DEVELOPER

Röst Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX
  • R

:: DOWNLOAD

DIAlignR

:: MORE INFORMATION

Citation

Gupta S, Ahadi S, Zhou W, Röst H.
DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.
Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: 10.1074/mcp.TIR118.001132. Epub 2019 Jan 31. PMID: 30705124; PMCID: PMC6442363.