Category: Alignment / BLAST

SOCS 2.2 – SOLiD Read Mapper with Bisulfite Sequencing Support

SOCS 2.2

:: DESCRIPTION

SOCS (short oligonucleotide color space) is a SOLiD read mapper with bisulfite sequencing support.SOCS performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. Modes are available for detecting short sequence-space variants (such as SNPs) and for detecting unlimited numbers of bisulfite-induced nucleotide substitutions for 5mC methylation studies.

::DEVELOPER

Nicholas H. Bergman (nickbergman@gatech.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SOCS

:: MORE INFORMATION

Citation

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.
Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH.
Bioinformatics. 2010 Aug 1;26(15):1901-2. doi: 10.1093/bioinformatics/btq291.

ParaTree – Parametric Alignment of Trees

ParaTree

:: DESCRIPTION

ParaTree is a parametric tool for aligning two ordered trees. There are two versoins depending on whether gap penalty is considered.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /Linux/MacOsX
  • Java

:: DOWNLOAD

 ParaTree

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Nov 22;19(17):2237-45.
Parametric alignment of ordered trees.
Wang L, Zhao J.

ScalaBLAST 2.4.53 – Multiprocessor Implementation of the NCBI BLAST library

ScalaBLAST 2.4.53

:: DESCRIPTION

ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. ScalaBLAST supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, or XML).

:: DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • gcc
  • MPI

:: DOWNLOAD

 ScalaBLAST

:: MORE INFORMATION

Citation

Oehmen, C.S. and J. Nieplocha. 2006.
“ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis“,
IEEE Transactions on Parallel and Distributed Systems, 17(8): 740-749.

Bioinformatics. 2013 Mar 15;29(6):797-8. doi: 10.1093/bioinformatics/btt013. Epub 2013 Jan 29.
ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems.
Oehmen CS, Baxter DJ.

MCScanX / MCScanX-transposed – Scan multiple Genomes to Identify Homologous Chromosomal Regions and more

MCScanX/ MCScanX-transposed

:: DESCRIPTION

MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity and extends the software by incorporating 15 utility programs for display and further analyses.

MCScanX-transposed: detecting transposed gene duplications based on multiple collinearity scans

::DEVELOPER

Haibao Tang : bao at uga dot edu and  Yupeng Wang: wyp1125@gmail.com at Plant Genome Mapping Laboratory, University of Georgia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • Java

:: DOWNLOAD

MCScanX / MCScanX-transposed

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1458-60. doi: 10.1093/bioinformatics/btt150. Epub 2013 Mar 28.
MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans.
Wang Y1, Li J, Paterson AH.

Nucleic Acids Res. 2012 Apr;40(7):e49. doi: 10.1093/nar/gkr1293. Epub 2012 Jan 4.
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH.

SECISaln 1.0 – Create Structure-based Alignments of an extensive dataset of Eukaryotic SECIS Sequences

SECISaln 1.0

:: DESCRIPTION

SECISaln predicts eukaryotic SECIS elements in a sequence and aligns them against a precompiled database of eukaryotic SECIS elements.

::DEVELOPER

RODERIC GUIGO LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No. Only web service.

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 1;25(5):674-5. Epub 2009 Jan 29.
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.
Chapple CE, Guigó R, Krol A.

gff2aplot 2.0 – Visualizing Pair-wise Alignments with Annotated Axes from GFF files.

gff2aplot 2.0

:: DESCRIPTION

gff2aplot is a program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.

::DEVELOPER

gff2aplot Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 gff2aplot 

:: MORE INFORMATION

Citation

Abril, J.F., Guigó, R. and Wiehe, T.
“gff2aplot: Plotting sequence comparisons.”
Bioinformatics, 19(18):2477-2479 (2003).

TwinCons – Alignment Score for detection of Ancient Homologies

TwinCons

:: DESCRIPTION

TwinCons is a software to detect noisy signals of deep ancestry of proteins or nucleic acids.

::DEVELOPER

The Williams Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TwinCons

:: MORE INFORMATION

Citation

Penev PI, Alvarez-Carreño C, Smith E, Petrov AS, Williams LD.
TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
PLoS Comput Biol. 2021 Oct 29;17(10):e1009541. doi: 10.1371/journal.pcbi.1009541. PMID: 34714829; PMCID: PMC8580257.

find_max_cover – Determine the best Combination of Local Alignments to a Query Sequence

find_max_cover

:: DESCRIPTION

find_max_cover  (FindMaxCover) finds the combination of local alignments that covers the maximum number of residues in a query sequence.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 find_max_cover

:: MORE INFORMATION

Citation

Conant, G. C., and A. Wagner, (2004)
A fast algorithm for determining the best combination of local alignments to a query sequence,
BMC Bioinformatics, 5: 62.

Minimap2 v2.23 – Pairwise Alignment for Nucleotide Sequences

Minimap2 v2.23

:: DESCRIPTION

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Minimap2

:: MORE INFORMATION

Citation

Li H.
New strategies to improve minimap2 alignment accuracy.
Bioinformatics. 2021 Oct 8:btab705. doi: 10.1093/bioinformatics/btab705. Epub ahead of print. PMID: 34623391.

Li H.
Minimap2: pairwise alignment for nucleotide sequences.
Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PMID: 29750242; PMCID: PMC6137996.

ProSeqViewer 1.0.42 – Visualize Sequence and Multiple Sequence Alignment (MSA)

ProSeqViewer 1.0.42

:: DESCRIPTION

ProSeqViewer is a TypeScript library to visualize annotation on single sequences and multiple sequence alignments.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • JS

:: DOWNLOAD

ProSeqViewer

:: MORE INFORMATION

Citation:

Bevilacqua M, Paladin L, Tosatto SCE, Piovesan D.
ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications.
Bioinformatics. 2021 Nov 12:btab764. doi: 10.1093/bioinformatics/btab764. Epub ahead of print. PMID: 34788797.