Tag: Searching

morePhyML 1.14 – Improving ML tree searching with PhyML 3

morePhyML 1.14

:: DESCRIPTION

morePhyML has been implemented to improve ML tree space exploration with PhyML. morePhyML allows inferring more accurate phylogenetic trees than several other recently developed ML tree inference softwares in many cases.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 morePhyML

:: MORE INFORMATION

Citation:

Criscuolo A. (2011)
morePhyML: improving the phylogenetic tree space exploration with PhyML 3.
Mol Phylogenet Evol. 61(3):944-8.

Cas-OFFinder 2.4.1 – Off-target Searching tool

Cas-OFFinder 2.4.1

:: DESCRIPTION

Cas-OFFinder searches for potential off-target sites in a given genome or user-defined sequences.

::DEVELOPER

Genome Engineering Lab. Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX

:: DOWNLOAD

 Cas-OFFinder 

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 15;30(10):1473-5. doi: 10.1093/bioinformatics/btu048. Epub 2014 Jan 24.
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases.
Bae S1, Park J, Kim JS.

MaRe – Searching and large scale Retrieval of public Microarray data

MaRe

:: DESCRIPTION

MaRe (Microarray Retriever) enables batch retrieval of microarray data matching your search criteria from the seas of data in GEO and ArrayExpress microarray repositories. You can search on accession numbers (GSE, GDS, AE_ACCN, PMID), authors, species, dates, platforms or on keywords of unspecified type.

::DEVELOPER

MaRe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W327-31. doi: 10.1093/nar/gkn213. Epub 2008 May 7.
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data.
Ivliev AE1, ‘t Hoen PA, Villerius MP, den Dunnen JT, Brandt BW.

NASSAM – 3D Pattern Searching in Nucleic Acid Structures

NASSAM

:: DESCRIPTION

The NASSAM (Nucleic Acid Search for Substructures And Motifs) program searches for 3D motifs and patterns of bases in RNA (and RNA associated) PDB formatted query structures.

::DEVELOPER

The Molecular Function Regulation Lab (M. Firdaus Raih research group)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hazrina Y. Hamdani, Sri D. Appasamy, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012.
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules.
Nucleic Acids Research. doi: 10.1093/nar/gks513.

PrimerFactoryQt 1.0.3 beta- Tool for Searching and Designing Primers

PrimerFactoryQt 1.0.3 beta

:: DESCRIPTION

PrimerFactoryQt is a tool for searching and designing primers. The Primer Search is based on Bowtie, an ultrafast, memory-efficient alignment program for aligning short DNA sequence. You can build your specific oligo database and search it against your query sequence. Consequently you find out, where your available primers will bind. Laboriously quests or new ordering of oligos is not anymore required. In addition you can save the search hits as features in a genbank file format.

::DEVELOPER

Stefanie Lück

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PrimerFactoryQt

:: MORE INFORMATION

MMseqs2 R13 – ultra Fast and Sensitive Protein Search and Clustering suite

MMseqs2 R13

:: DESCRIPTION

MMseqs2 (Many-against-Many sequence searching) is a software suite for very fast protein sequence searches and clustering of huge protein sequence data sets.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
:: DOWNLOAD

 MMseqs2

:: MORE INFORMATION

Citation:

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets.
Hauser M, Steinegger M, Söding J.
Bioinformatics. 2016 Jan 6. pii: btw006.

Steinegger M and Soeding J.
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
Nature Biotechnology, doi: 10.1038/nbt.3988 (2017).

SWIFT 1.0.1 / BALSAM 1.3 – Fast Local Alignment Searching

SWIFT 1.0.1 / BALSAM 1.3

:: DESCRIPTION

SWIFT suit is a software collection for fast index-based sequence comparison. It contains the following programs:

  • SWIFT — fast local alignment search, guaranteeing to find epsilon-matches between two sequences.
  • SWIFT BALSAM (BAsic fiLter for Semigobal non-gapped AlignMent search) — a very fast program to find semiglobal non-gapped alignments based on k-mer seeds.

::DEVELOPER

Wolfgang Gerlach ; Rasmussen KR, Stoye J, Myers EW.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / SUN solaris

:: DOWNLOAD

SWIFT ; BALSAM

:: MORE INFORMATION

Citation

K. Rasmussen, J. Stoye, E. W. Myers

Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length
In J. Comp. Biol. 13(2), 296-308, 2006.

Wregex 2.1 – Amino Acid Motif searching

Wregex 2.1

:: DESCRIPTION

Wregex (weighted regular expression).is a software tool for amino acid motif searching.

::DEVELOPER

EhuBio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Wregex

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1220-7. doi: 10.1093/bioinformatics/btu016. Epub 2014 Jan 9.
Prediction of nuclear export signals using weighted regular expressions (Wregex).
Prieto G1, Fullaondo A, Rodriguez JA.

RNAMotifScan 5.3 – Automatic Comparing and Searching for RNA Tertiary Motifs

RNAMotifScan 5.3

:: DESCRIPTION

RNAMotifScan is a tool for automatic comparing and searching for RNA tertiary motifs using secondary structural alignment.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • C Compiler

:: DOWNLOAD

 RNAMotifScan

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Oct;38(18):e176. doi: 10.1093/nar/gkq672. Epub 2010 Aug 8.
RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.
Zhong C, Tang H, Zhang S.