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 1.4 – MOtif Discovery in Nucleotide Sequences from Co-regulated Genes

Pscan 1.4

:: 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.

BlastAlign 1.4 – Use Blast to Align Problematic Nucleotide Sequences

BlastAlign 1.4

:: DESCRIPTION

BlastAlign uses NCBI Blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align globally. The program selects the most representative sequence from the input sequences and then extracts the blast query anchored multiple alignment (in NEXUS and Phylip formats). Alternatively, the user can choose which sequence to use as an anchor. The program also outputs a matrix representing regions of homology along the sequences, which can be used to visually identify subgroups sharing particular large indels. An additional program, BlastAlignP uses tblastn to align nucleotide sequences to a single amino acid reference sequence, allowing an open reading frame to be maintained in the multiple alignment.

::DEVELOPER

Aris Katzourakis and Robert Belshaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BlastAlign

:: MORE INFORMATION

Citation:

Belshaw R, Katzourakis A. 2005.
BlastAlign: a program that uses blast to align problematic nucleotide sequences.
Bioinformatics 21:122-3

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

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

TranslatorX – Nucleotide Sequence Alignment and Alignment Cleaning based on Amino Acid Information

TranslatorX

:: DESCRIPTION

 TranslatorX is a tool to align (protein-coding) nucleotide sequences based on the corresponding amino acid alignments. Given a set of nucleotide sequences, TranslatorX translates them to amino acids using the appropriate genetic code, aligns those amino acid sequences and, from the resulting alignment, determines the optimal alignment of nucleotide sequences.

::DEVELOPER

Federico Abascal

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TranslatorX

:: MORE INFORMATION

Citation:

Abascal F, Zardoya R, Telford MJ (2010)
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
Nucleic Acids Res. 38:W7-13.

 

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.