Tag: Finder

IRF 3.07 – Inverted Repeats Finder

IRF 3.07

:: DESCRIPTION

IRF(Inverted Repeats Finder) investigate inverted repeat structure of the Human Genome

::DEVELOPER

Laboratory for Biocomputing and Informatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 IRF

:: MORE INFORMATION

Citation:

P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson.
“Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes” ,
Genome Research, 14:1861-1869, 2004.

SLIF 2-2 – Subcellular Location Image Finder

SLIF 2-2

:: DESCRIPTION

SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution.

::DEVELOPER

Murphy Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Matlab
  • Java

:: DOWNLOAD

 SLIF

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 15;24(4):569-76.
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models.
Qian Y, Murphy RF.

SNPPar V1.0 – Parallel/Homoplasic SNP Finder

SNPPar V1.0

:: DESCRIPTION

SNPPar is designed to find homoplasic SNPs based on a user-defined phylogenetic tree

::DEVELOPER

SNPPar team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SNPPar

:: MORE INFORMATION

Citation

Edwards DJ, Duchene S, Pope B, Holt KE.
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.
Microb Genom. 2021 Dec;7(12). doi: 10.1099/mgen.0.000694. PMID: 34874243.

LargeDEL 0.1 – A large Deletion Finder tool

LargeDEL 0.1

:: DESCRIPTION

LargeDEL is a software to find large deletions on the aligned whole genome sequence data. It is also capable of extracting the candidate deletions according to desired criteria.

::DEVELOPER

Advanced Genomics and Bioinformatic Research Group, İGBAM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

LargeDEL

:: MORE INFORMATION

FirstEF – Human First Exon Finder

FirstEF

:: DESCRIPTION

FirstEF (First Exon Finder) is a 5′ terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. The probabilistic models are optimized to find potential first donor sites and CpG-related and non-CpG-related promoter regions based on discriminant analysis. For every potential first donor site (GT) and an upstream promoter region, FirstEF decides whether or not the intermediate region can be a potential first exon, based on a set of quadratic discriminant functions.

::DEVELOPER

Michael Zhang Computational Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Computational identification of promoters and first exons in the human genome.
Davuluri RV, Grosse I, Zhang MQ.
Nat Genet. 2001 Dec;29(4):412-7. Erratum in: Nat Genet 2002 Nov;32(3):459.

bcfind 1.0 – Brain cell finder

bcfind 1.0

:: DESCRIPTION

bcfind is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy.

::DEVELOPER

bcfind team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
:: DOWNLOAD
 bcfind

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Sep 1;30(17):i587-i593. doi: 10.1093/bioinformatics/btu469.
Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images.
Frasconi P, Silvestri L, Soda P, Cortini R, Pavone FS, Iannello G.

CSMinFinder – Chromatin State with Minimum length Finder

CSMinFinder

:: DESCRIPTION

CSMinFinder is a linear time algorithm for calculating a set of non-overlapping regions that maximizes the sum of similarities between the vector of focal epigenetic states and the vectors of raw epigenetic states at DNA positions in the set of regions.

::DEVELOPER

Morishita Laboratory, the University of Tokyo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

CSMinFinder

:: MORE INFORMATION

Citation

A linear time algorithm for detecting long genomic regions enriched with a specific combination of epigenetic states.
Ichikawa K, Morishita S.
BMC Genomics. 2015;16 Suppl 2:S8. doi: 10.1186/1471-2164-16-S2-S8

HUF-ZINC – HMM-based U-shape Motif Finder for Zinc Binding

HUF-ZINC

:: DESCRIPTION

HUF-ZINC is a HMM-based web server for prediction of the novel, as well as conventional, zinc finger motifs in protein sequences.

::DEVELOPER

Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340008. doi: 10.1142/S0219720013400088. Epub 2013 Jan 16.
Motif discovery with data mining in 3D protein structure databases: discovery, validation and prediction of the U-shape zinc binding (“Huf-Zinc”) motif.
Maurer-Stroh S1, Gao H, Han H, Baeten L, Schymkowitz J, Rousseau F, Zhang L, Eisenhaber F.

FusionCatcher 1.33 – Fusion Genes Finder for RNA-seq data

FusionCatcher 1.33

:: DESCRIPTION

FusionCatcher searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

::DEVELOPER

FusionCatcher team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • Biopyton
  • Bowtie

:: DOWNLOAD

 FusionCatcher

:: MORE INFORMATION

Citation

S. Kangaspeska, S. Hultsch, H. Edgren, D. Nicorici, A. Murumägi, O.P. Kallioniemi,
Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms,
PLoS ONE 7(10): e48745. doi:10.1371/journal.pone.0048745

UPF 0.912 – Unique Peptide Finder

UPF 0.912

:: DESCRIPTION

UPF is used to calculate sets of unique peptides from protein sequences. Furthermore, UPF provides the possibility to calculate both the frequency of peptides and to retrieve information from which proteins a particular peptide can be derived.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

upf

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 UPF

:: MORE INFORMATION

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