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.

Censor 4.2.29 – Compares and Masks Protein or Nucleotide Sequences

Censor 4.2.29

:: DESCRIPTION

CENSOR is a software tool which screens query sequences against a reference collection of repeats and “censors” (masks) homologous portions with masking symbols, as well as generating a report classifying all found repeats.

:: DEVELOPER

Genetic Information Research Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Censor

:: MORE INFORMATION

Citation:

Kohany O, Gentles AJ, Hankus L, Jurka J
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
BMC Bioinformatics, 2006 Oct 25;7:474

Cluster-Buster 20100219 – Find Dense Clusters of Motifs in Nucleotide Sequences

Cluster-Buster 20100219

:: DESCRIPTION

Cluster-Buster is the third generation program for finding clusters of pre-specified motifs in nucleotide sequences. The main application is detection of sequences that regulate gene transcription, such as enhancers and silencers, but other types of biological regulation may be mediated by motif clusters too.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

Web version:

:: REQUIREMENTS

  • Windows with CygWin / Linux / Mac OsX

:: DOWNLOAD

Cluster-Buster

:: MORE INFORMATION

Citation:

Martin C Frith, Michael C Li, and Zhiping Weng (2003). Cluster-Buster: Finding dense clusters of motifs in DNA sequencesNucleic Acids Research, 31(13):3666-8.

 

qnr 0.8067 – Discover Fluoroquinolone Antibiotic Resistance (qnr) Genes in Fragmented Nucleotide Sequences

qnr 0.8067

:: DESCRIPTION

qnr is a Python implementation of a method for searching large metagenomic dataset to identify qnr fluoroquinolone antibiotic resistance genes.

::DEVELOPER

qnr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 qnr

:: MORE INFORMATION

Citation:

A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences.
Boulund F, Johnning A, Pereira MB, Larsson DG, Kristiansson E.
BMC Genomics. 2012 Dec 11;13:695. doi: 10.1186/1471-2164-13-695.

Pscan 1.5 – MOtif Discovery in Nucleotide Sequences from Co-regulated Genes

Pscan 1.5

:: DESCRIPTION

Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences. Pscan does not resort to comparisons with orthologous sequences and experimental results show that it compares favorably to other tools for the same task in terms of false positive predictions and computation time.

::DEVELOPER

Bioinformatics Evolution @nd COmparative geNomics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Pscan

:: MORE INFORMATION

Citation:

F.Zambelli, G.Pesole, G.Pavesi
Pscan: Finding Over-represented Transcription Factor Binding Site Motifs in Sequences from Co-Regulated or Co-Expressed Genes.
Nucleic Acids Research 2009 37(Web Server issue):W247-W252.

JFreq – Frequencies of Short Nucleotide Sequences

JFreq

:: DESCRIPTION

JFreq (Java Word Frequencies) is a front end to Schbath’s R’MES, which is available at the R’MES website. R’MES finds the expected and actual frequencies of short nucleotide sequences, or words, using a Markov model to control for the effects of base composition and the frequencies of shorter words. Unusually frequent or infrequent occurrences of certain words may indicate biological relevance. For example, if the word “TAATTT” occurs much less frequently than expected, it might be that it performs some regulatory function, or makes the sequence vulnerable to mutation, or has some other biological function.

::DEVELOPER

Dr. Chris Upton, University of Victoria, Biochemistry and Microbiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JFreq

:: MORE INFORMATION

PatSearch – Detection of Patterns and Structural Motifs in Nucleotide Sequences

PatSearch

:: DESCRIPTION

PatSearch is a pattern matching tool for database searching of composite motifs including regular expression patterns, secondary structure elements, nucleotide weight matrices (e.g. TRANSFAC matrices)  and allowing mismatches and/or mispairings below a user-fixed threshold;

::DEVELOPER

the Research Network of Bioinformatics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences.
Grillo G, Licciulli F, Liuni S, Sbisà E, Pesole G.
Nucleic Acids Res. 2003 Jul 1;31(13):3608-12.

BWT-SW 20080713 – Local Alignment tool for searching Nucleotide Sequences

BWT-SW 20080713

:: DESCRIPTION

BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments , BWT-SW finds all local alignments1. The running speed of BWT-SW depends on the lengths of the database sequence and the query sequence. On a set of experiments using human genome as the database sequence, BWT-SW takes the same order of time as BLASTn on query sequences of length 1000 nucleotides or less  . As far as we know, BWT-SW is the first practical tool that can find all local alignments.

::DEVELOPER

C.K. Wong (ckwong3@cs.hku.hk)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  BWT-SW

:: MORE INFORMATION

Citation:

T.W. Lam; W.K. Sung; S.L. Tam; C.K. Wong; S.M. Yiu.
Compressed Indexing and Local Alignment of DNA
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn032

PatMatch 1.2 – Find Patterns in Peptide and Nucleotide Sequences

PatMatch 1.2

:: DESCRIPTION

 PatMatch (Pattern Matching) allows you to search for short (<20 residues) nucleotide or peptide sequences, or ambiguous/degenerate patterns. It uses the same Arabidopsis dataset as TAIR’s BLAST and FASTA programs. If you are searching for a sequence >20 bp or aa with no degenerate positions, please use BLAST or FASTA, which are much faster. Pattern Matching allows for ambiguous characters, mismatches, insertions and deletions, but does not do alignments and so is not a replacement for BLAST and FASTA Currently the maximum number of hits retrieved is 250,000 and the minimum number of input string is 3 residues.

::DEVELOPER

The Arabidopsis Information Resource

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PatMatch

:: MORE INFORMATION

Citation:

Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee SY.
PatMatch: a program for finding patterns in peptide and nucleotide sequences.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W262-6.

AnnHyb 4.946 / PyAnnHyb 0.021 – Manage Nucleotide Sequences

AnnHyb 4.946 / PyAnnHyb 0.021

:: DESCRIPTION

AnnHyb is a tool for working with and managing nucleotide sequences in multiple formats.The features include sequence viewer, sequence editor, sequence annotation, format conversion, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi-alignment viewer, consensus determination…

PyAnnHyb rewrite the complete AnnHyb application using the Python programming language in order to run under various platforms like Linux, Mac OS X and Microsoft-Windows.

::DEVELOPER

Olivier Friard

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • python

:: DOWNLOAD

AnnHybPyAnnHyb

:: MORE INFORMATION

AnnHyb is free software, and is released under the GNU General Public License.

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