Tag: Filter

DiagAF 21.2.7 – Pre-Alignment Filter for Sequence Alignment

DiagAF 21.2.7

:: DESCRIPTION

DiagAF is a more accurate and efficient pre-alignment filter for sequence alignment. It can efficiently filter out candidates that contain errors greater than the edit distance threshold during read mapping.

::DEVELOPER

DiagAF team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DiagAF

:: MORE INFORMATION

Citation

Yu C, Zhao Y, Zhao C, Ma H, Wang G.
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Nov 17;PP. doi: 10.1109/TCBB.2021.3127879. Epub ahead of print. PMID: 34780330.

MiRTif – MicroRNA:Target Interaction Filter

MiRTif

:: DESCRIPTION

MiRTif is a machine learning algorithm based on SVM (support vector machine) that serves as a post-processing filter for the miRNA:target duplexes predicted by softwares such as miRanda, PicTar and TargetScanS.

::DEVELOPER

the Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MiRTif: a support vector machine-based microRNA target interaction filter.
Yang Y, Wang YP, Li KB.
BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S4. doi: 10.1186/1471-2105-9-S12-S4.

TuRF-E 1.0 – Gene-gene Interaction Giltering with Ensemble of Filters

TuRF-E 1.0

:: DESCRIPTION

Providing TuRF-E program for SNP interaction filtering.

::DEVELOPER

TuRF-E team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Perl
:: DOWNLOAD

 TuRF-E

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S10. doi: 10.1186/1471-2105-12-S1-S10.
Gene-gene interaction filtering with ensemble of filters.
Yang P1, Ho JW, Yang YH, Zhou BB.

DNMFilter 0.1.1 – De Novo Mutation Filter

DNMFilter 0.1.1

:: DESCRIPTION

DNMFilter is a machine learning based tool designed to filter out false positive de novo mutations (DNMs) obtained by any computational or manual approaches from next generation sequencing data.

::DEVELOPER

DNMFilter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Python

:: DOWNLOAD

 DNMFilter

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 27.
A gradient-boosting approach for filtering de novo mutations in parent-offspring trios.
Liu Y1, Li B, Tan R, Zhu X, Wang Y.

AgileGeneFilter 20120105 – Allows Sequence Variants to be Filtered

AgileGeneFilter 20120105

:: DESCRIPTION

AgileGeneFilter allows sequence variants exported from AgileVariantViewer or AgileAnnotator to be filtered, by first identifying the proteins that are affected by the sequence variants and then performing a textual data search on these proteins, using information downloaded from the UNI-Prot web page.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileGeneFilter

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AgileGeneFilter

:: MORE INFORMATION

AgileVariantViewer 20120105 – Allows Sequence Variants to be interactively Displayed and Filtered

AgileVariantViewer 20120105

:: DESCRIPTION

AgileVariantViewer allows sequence variants to be interactively displayed and filtered.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileVariantViewer

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AgileVariantViewer

:: MORE INFORMATION

SWATH2stats 1.22.0 – Transform and Filter SWATH Data for Statistical Packages

SWATH2stats 1.22.0

:: DESCRIPTION

SWATH2stats is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.

::DEVELOPER

Aebersold Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R / BioConductor

:: DOWNLOAD

 SWATH2stats

:: MORE INFORMATION

Citation

PLoS One. 2016 Apr 7;11(4):e0153160. doi: 10.1371/journal.pone.0153160. eCollection 2016.
SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.
Blattmann P, Heuse M, Aebersold R.

BioBloomTools 2.3.3 – Fast Sequence Categorization tool utilizing Bloom filters

BioBloomTools 2.3.3

:: DESCRIPTION

BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorizes sequences. This methodology is faster than alignment but does not provide mapping locations. BBT was initially intended to be used for pre-processing and QC applications like contamination detection, but is flexible to accommodate other purposes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 BioBloom Tools

:: MORE INFORMATION

Citation

BioBloom Tools: Fast, accurate and memory-efficient host species sequence screening using Bloom filters.
Chu J, Sadeghi S, Raymond A, Jackman SD, Nip KM, Mar R, Mohamadi H, Butterfield YS, Robertson AG, Birol I.
Bioinformatics. 2014 Aug 20. pii: btu558.

SortMeRNA 2.1 – Filter rRNA Fragments from Metatranscriptomic data

SortMeRNA 2.1

:: DESCRIPTION

SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • C++ Compiler

:: DOWNLOAD

 SortMeRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611.
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
Kopylova E, Noé L, Touzet H.

RNAsifter 1.0 – RNA Shape Index Filter

RNAsifter 1.0

:: DESCRIPTION

RNAsifter is a non-rigorous filter for the rfam database, that is based on the abstract shape approach. It exploits the familily specific secondary structure, i.e. it computes shapes for the query-sequence and compares them to a precalculated shape-index. The exact matches deliver – hopefully only few – candiate families in which the query-sequence might fold. Membership for the candidate families is checked with the program cmsearch, afterwards.

::DEVELOPER

S. Janssen, J. Reeder and R. Giegerich.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • perl

:: DOWNLOAD

RNAsifter

:: MORE INFORMATION

Citation

S. Janssen, J. Reeder and R. Giegerich.
Shape based indexing for faster search of RNA family databases.
BMC Bioinformatics. 2008 Feb 29;9:131.