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Pairwise sequence alignment software tools | Protein comparison analysis

Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference…
AlignMe
Web
Desktop

AlignMe Alignment of Membrane Proteins

Permits pair-wise (PW) alignment of membrane proteins. AlignMe takes into…

Permits pair-wise (PW) alignment of membrane proteins. AlignMe takes into account membrane-specific information in the form of transmembrane predictions, or hydrophobicity scales, while constructing…

G T A T C G C T A
SPALN
Web
Desktop

SPALN

Allows users to map and align cDNA or protein sequences onto a whole genomic…

Allows users to map and align cDNA or protein sequences onto a whole genomic sequence (WGS). Spaln intends to improve automatic classification of alternative splicing and transcriptional initiation…

iPBA
Web

iPBA

A tool for comparison of protein structures based on similarity in the local…

A tool for comparison of protein structures based on similarity in the local backbone conformation.

HOMEP
Dataset

HOMEP HOmologous MEmbrane Proteins dataset

Generates alignments or build models of these proteins, using other…

Generates alignments or build models of these proteins, using other 'family' members as templates, and compares the results with the known structures and/or alignments. HOMEP is a benchmark…

HMMsato
Desktop

HMMsato

Provides a method for improving profile-profile alignments. HMMsato binds…

Provides a method for improving profile-profile alignments. HMMsato binds torsion angles, relative solvent accessibility and evolutionary residue into Hidden Markov Mode (HMM)-based pairwise…

Rigapollo
Desktop

Rigapollo

Allows pairwise alignment. Rigapollo is based on a Support Vector Machine…

Allows pairwise alignment. Rigapollo is based on a Support Vector Machine (SVM)-dependent Hidden Markov Model (HMM) method. It can generate pairwise alignments based on any set of (user-defined)…

FsePSA
Desktop

FsePSA

Computes pairwise alignments between coding sequences while accounting for the…

Computes pairwise alignments between coding sequences while accounting for the length of frameshift translations. FsePSA is a python package that is particularly robust to parameter changes as…

MOSAL
Web
Desktop

MOSAL MultiObjective Sequence Alignment Tools

A pruning technique for improving the performance of dynamic programming…

A pruning technique for improving the performance of dynamic programming algorithms for bicriteria pairwise sequence alignment, which uses lower and upper bounds to discard states in early stages of…

Ngila
Desktop

Ngila

A global alignment program that can align pairs of sequences using logarithmic…

A global alignment program that can align pairs of sequences using logarithmic and affine gap penalties.

SFESA
Web

SFESA Shift to Fix secondary structure ElementS in Alignments

A tool to refine pairwise protein sequence alignment, with a combination of…

A tool to refine pairwise protein sequence alignment, with a combination of sequence and structural scoring by locally shifting secondary structure elements. Taking a pairwise alignment as input, the…

PROPER
Desktop

PROPER PROtein-protein interaction network alignment based on PERcolatin

Offers a global pairwise-network alignment algorithm dedicated to…

Offers a global pairwise-network alignment algorithm dedicated to protein-protein interactions (PPIs). PROPER aims to align social graphs from different domains. It is based on a two-stage procedure:…

ALN
Web
Desktop

ALN

Allows alignment of a pair of nucleotide, amino acid sequences or groups of…

Allows alignment of a pair of nucleotide, amino acid sequences or groups of sequences. ALN is a spliced alignment program that can use a generalized profile as template.

Exonerate
Desktop

Exonerate

A generic tool for pairwise sequence comparison. Exonerate allows you to align…

A generic tool for pairwise sequence comparison. Exonerate allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics. The Exonerate…

MTRAP
Desktop

MTRAP Measure based on TRAnsition Probability

Minimizes the value of a certain objective function based on the transition…

Minimizes the value of a certain objective function based on the transition quantity. MTRAP is an alignment algorithm based on a metric determined by an adjusted substitution matrix and a transition…

PATH
Web

PATH

A tool that addresses the problem of finding distant protein homologies where…

A tool that addresses the problem of finding distant protein homologies where the divergence is the result of frameshift mutations and substitutions.

PR2ALIGN
Desktop
Web

PR2ALIGN

A stand-alone software program and a web-server that provide the functionality…

A stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on…

GapMis
Desktop

GapMis

A tool for pairwise sequence alignment with a single gap.

A tool for pairwise sequence alignment with a single gap.

nw
Desktop

nw

Permits sequence alignments. nw is based on the Needleman and Wunsch algorithm.…

Permits sequence alignments. nw is based on the Needleman and Wunsch algorithm. It returns sequence similarity calculated in different ways.

neobio
Desktop

neobio

Provides a library gathering bioinformatics algorithms. Neobio mainly supplies…

Provides a library gathering bioinformatics algorithms. Neobio mainly supplies sequence alignment algorithms. The Application Programming Interface (API) is composed of three packages which allows…

PASA
Desktop

PASA Program to Assemble Spliced Alignments

Allows automation improvement of gene structures in Arabidopsis thaliana. PASA…

Allows automation improvement of gene structures in Arabidopsis thaliana. PASA was used in Eukaryotic genome annotation projects such as Rice, Aspergillus species, Plasmodium falciparum, Schistosoma…

JAligner
Web
Desktop

JAligner

Aligns biological pairwise sequences. JAligner uses affine gap penalty model to…

Aligns biological pairwise sequences. JAligner uses affine gap penalty model to proceed.

SIAS
Web

SIAS Sequence Identity And Similarity

Calculates pairwise sequence identity and similarity from multiple sequence…

Calculates pairwise sequence identity and similarity from multiple sequence alignments.

SIM
Web

SIM

Finds best non-intersecting alignments between two sequences or within a…

Finds best non-intersecting alignments between two sequences or within a sequence using dynamic programming techniques. SIM is an online method and a time-efficient algorithm. The alignments are…

Needle
Web

Needle

Reads two input sequences and writes their optimal global sequence alignment to…

Reads two input sequences and writes their optimal global sequence alignment to file.

NW-align
Web

NW-align

Simple and robust alignment program for protein sequence-to-sequence alignments…

Simple and robust alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm.

ApicoAlign
Web

ApicoAlign

Finds orthologs and aligns apicomplexan proteins using a novel series of…

Finds orthologs and aligns apicomplexan proteins using a novel series of matrices. ApicoAlign can be used for five applications (1) Search Database (2) Search a genome (3) Reciprocal Hit (4) Best…

CASA
Web

CASA

Evaluates the accuracy of protein sequence alignment methods. CASA is an…

Evaluates the accuracy of protein sequence alignment methods. CASA is an implementation of the alignment accuracy benchmark. The server produces graphical and tabular comparisons of the accuracy of a…

NdPASA
Web

NdPASA

Employs neighbor-dependent propensities of amino acids as a unique parameter…

Employs neighbor-dependent propensities of amino acids as a unique parameter for alignment. NdPASA is a method for pairwise sequence alignment. It optimizes alignment by evaluating the likelihood of…

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