Tag: Pairwise Alignment

iPARTS 2 – A Tool of Improved/ Pairwise Alignment of RNA Tertiary Structures

iPARTS2

:: DESCRIPTION

iPARTS2 (improved PARTS) is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach.

::DEVELOPER

Chih-Wei Wang, Kun-Tze Chen and Chin Lung Lu.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yang CH, Shih CT, Chen KT, Lee PH, Tsai PH, Lin JC, Yen CY, Lin TY, Lu CL.
iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.
Nucleic Acids Res. 2016 Jul 8;44(W1):W328-32. doi: 10.1093/nar/gkw412. Epub 2016 May 16. PMID: 27185896; PMCID: PMC4987943.

iPARTS: an improved tool of pairwise alignment of RNA tertiary structures.
Wang CW, Chen KT, Lu CL.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W340-7. doi: 10.1093/nar/gkq483.

HH-suite v3.3.0 – Remote Protein Homology Detection suite

HH-suite v3.3.0

:: DESCRIPTION

The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 HH-suite

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2015 Oct 23;11(10):e1004343. doi: 10.1371/journal.pcbi.1004343. eCollection 2015.
Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.
Meier A, Söding J

Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019)
HH-suite3 for fast remote homology detection and deep protein annotation,
BMC Bioinformatics, 473. doi: 10.1186/s12859-019-3019-7

ALIGN 2.0 – Pairwise Alignment

ALIGN 2.0

:: DESCRIPTION

ALIGN (Pairwise alignment) is a tool designed for performing sequence alignments in a wide variety of combinations. It implements sequence to sequence, sequence to profile and profile to profile alignments with optional support of secondary structure. Different alignment options are freely selectable and include alignment types (local, global, free-shift) and number of sub-optimal results to report.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 ALIGN

:: MORE INFORMATION

Citation:

Curr Drug Discov Technol. 2006 Sep;3(3):167-73.
Align: a C++ class library and web server for rapid sequence alignment prototyping.
Tosatto SC, Albiero A, Mantovan A, Ferrari C, Bindewald E, Toppo S.

ALN 3.5.2 – Pairwise Alignment of Biological Sequences Supporting Spliced Alignment Procedures

ALN 3.5.2

:: DESCRIPTION

Aln is a program for aligning a pair of nucleotide or amino acid sequences or groups of sequences. Aln accepts various combinations of distinct types of inputs: a single nucleotide sequence (SN), a single amino acid sequence (SA), a pre-aligned group of nucleotide sequences (MN), and a group of amino acid sequences (MA). Notably, aln can now perform mixed alignment between a nucleotide sequence and a protein sequence or a group of protein sequences [5]. This novel feature of aln enables us to predict eukaryotic gene structures (protein-coding exons) based on sequence homology with known protein sequence(s). The details of this procedure will be described in a later section entitled ‘Gene-structure prediction’.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 ALN

:: MORE INFORMATION

Citation

Gotoh, O. (2000)
” Homology-based gene structure prediction: simplified matching algorithm by the use of translated codon (tron) and improved accuracy by allowing for long gaps.”
Bioinformatics, 16, 190-202.

PCS 1.5 – Identify and Analyze Conserved K-mers in Pairwise Alignment

PCS 1.5

:: DESCRIPTION

PCS (Pairwise Conservation Scores) is stand-alone pakage to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3′-UTRs.

::DEVELOPER

Bioinformatics & Intelligent Information Processing Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Perl 

:: DOWNLOAD

 PCS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Nov 8;8:432.
Identifications of conserved 7-mers in 3′-UTRs and microRNAs in Drosophila.
Gu J, Fu H, Zhang X, Li Y.

rVista 2.0 – Identification of TFBS Conserved in Pairwise Alignments

rVista 2.0

:: DESCRIPTION

The rVISTA tool combines TFBS predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are evolutionarily conserved and present in a specific configuration within genomic sequences. The newly developed version 2.0 of the rVISTA tool can process alignments generated by both the zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from the ECR Browser and GALA database.

::DEVELOPER

Ivan Ovcharenko Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

rVISTA 2.0: evolutionary analysis of transcription factor binding sites.
Loots GG, Ovcharenko I.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W217-21.

G-PAS 2.0 – Fast GPU vesion of a Pairwise Alignment algorithms

G-PAS 2.0

:: DESCRIPTION

G-PAS (gpu-pairAlign) implements global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. Our solution performs the alignment of every given sequence pair, which is a required step e.g. for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions.

::DEVELOPER

G-PAS Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • g++ compiler
  • CUDA 2.0 or higher
  • CUDA-compliant GPU

:: DOWNLOAD

 G-PAS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 20;12:181.
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.
Blazewicz J, Frohmberg W, Kierzynka M, Pesch E, Wojciechowski P.

Alnpack 2.1 – C++ Library for Pairwise Local Alignment

Alnpack 2.1

:: DESCRIPTION

Alnpack is a set of programs and a C++ library for pairwise local alignment of DNA or protein sequences using Smith-Waterman algorithm.

:: DEVELOPER

Genetic Information Research Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C++ compiler

:: DOWNLOAD

  Alnpack

:: MORE INFORMATION

Citation:

Farrar M.
Striped Smith-Waterman speeds database searches six times over other SIMD implementations.
Bioinformatics. 2007 Jan 15;23(2):156-61. Epub 2006 Nov 16.