Tag: Identification

Cinteny – Server for Synteny Identification and Analysis of Genome Rearrangement

Cinteny

:: DESCRIPTION

Cinteny is a flexible and efficient tool for analysis of synteny and evolutionary distances in terms of genome rearrangements (the reversal distance) for multiple genomes. In addition to annotated genomes, which are available for interactive browsing and assessment of synteny and evolutionary distances in terms of orthologous genes, Cinteny can be used with user provided discrete objects, such as sequence tags or other evolutionarily conserved markers.

:: SCREENSHOTS

N/A

::DEVELOPER

Meller Lab

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Mar 8;8:82.
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms.
Sinha AU1, Meller J.

ICDMR – Identification of Consistently Differentially Methylated Regions

ICDMR

:: DESCRIPTION

ICDMR is an unsupervised approach, where there is no need to choose the comparative group in advance, and is able to identify methylation modifications either among individuals or between potential subgroups in a population.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 ICDMR

:: MORE INFORMATION

Citation

A novel method for identification and quantification of consistently differentially methylated regions.
Hsiao CL, Hsieh AR, Lian IeB, Lin YC, Wang HM, Fann CS.
PLoS One. 2014 May 12;9(5):e97513. doi: 10.1371/journal.pone.0097513

DMINDA 2.0 – DNA Motif Identification and Analyses

DMINDA 2.0

:: DESCRIPTION

DMINDA is an integrated web server for DNA motif identification and analyses

::DEVELOPER

Qin Ma  , Bioinformatic and Mathematical Biosciences Lab, The Ohio State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Yang J, Chen X, McDermaid A, Ma Q.
DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses.
Bioinformatics. 2017 Aug 15;33(16):2586-2588. doi: 10.1093/bioinformatics/btx223. PMID: 28419194.

DMINDA: an integrated web server for DNA motif identification and analyses.
Ma Q, Zhang H, Mao X, Zhou C, Liu B, Chen X, Xu Y.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W12-9. doi: 10.1093/nar/gku315.

TFBayes – Identification of Transcription Factor Binding Sites

TFBayes

:: DESCRIPTION

TFBayes is a software for bayesian analysis of ChIP-Seq data for the identification of transcription factor binding sites.

::DEVELOPER

Philipp Benner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TFBayes

:: MORE INFORMATION

Citation

Point estimates in phylogenetic reconstructions.
Benner P, Bačák M, Bourguignon PY.
Bioinformatics. 2014 Sep 1;30(17):i534-i540. doi: 10.1093/bioinformatics/btu461.

IDP-Seq2Seq – Identification of Intrinsically Disordered Proteins and Regions based on Sequence to Sequence Learning

IDP-Seq2Seq

:: DESCRIPTION

IDP-Seq2Seq applied the Sequence to Sequence Learning (Seq2Seq) derived from natural language processing (NLP) to map protein sequences to “semantic space” to reflect the structure patterns with the help of predicted Residue-Residue Contacts (CCMs) and other sequence-based features. Furthermore, the Attention mechanism was employed to capture the global associations between all residue pairs in the proteins.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Tang YJ, Pang YH, Liu B.
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning.
Bioinformatics. 2021 Jan 29;36(21):5177-5186. doi: 10.1093/bioinformatics/btaa667. PMID: 32702119.

iMiRNA-PseDPC – microRNA Precursor Identification with a Pseudo Distance-pair Composition Approach

iMiRNA-PseDPC

:: DESCRIPTION

The web-server iMiRNA-PseDPC was developed for identifying the real microRNA precursors and false microRNA precursors.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2015 Feb 3:1-28. [Epub ahead of print]
iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach.
Liu B1, Fang L, Liu F, Wang X, Chou KC.

eCAMI – Simultaneous Classification and Motif Identification for enzyme/CAZyme annotation

eCAMI

:: DESCRIPTION

eCAMI is a Python package: (i) has the best performance in terms of accuracy and memory use for CAZyme and enzyme EC classification and annotation; (ii) the k-mer-based tools (including PPR-Hotpep, CUPP and eCAMI) perform better than homology-based tools and deep-learning tools in enzyme EC prediction.

::DEVELOPER

YIN LAB @ UNL & ZHANG LAB @ NKU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

eCAMI

:: MORE INFORMATION

Citation

Xu J, Zhang H, Zheng J, Dovoedo P, Yin Y.
eCAMI: simultaneous classification and motif identification for enzyme annotation.
Bioinformatics. 2020 Apr 1;36(7):2068-2075. doi: 10.1093/bioinformatics/btz908. PMID: 31794006.

PhaseTank 1.0 – Genome-wide Computational Identification of phasiRNAs

PhaseTank 1.0

:: DESCRIPTION

PhaseTank is a software to systemically characterize phasiRNAs (Phase siRNAs)/tasiRNAs and their regulatory cascades ‘miRNA/phasiRNA  -> PHAS gene -> phasiRNAs -> target genes’ in plants.

::DEVELOPER

Qingli Guo, Northwest A&F University, guoql.karen@gmail.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PhaseTank

:: MORE INFORMATION

Citation

PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades.
Guo Q, Qu X, Jin W.
Bioinformatics. 2014 Sep 21. pii: btu628.

NAIBR – Novel Adjacency Identification with Barcoded Reads

NAIBR

:: DESCRIPTION

NAIBR is a probabilistic algorithm for the identification of novel adjacencies from whole-genome linked-read sequencing data. NAIBR takes as input a barcoded and phased BAM processed with 10X Genomics’ “Long Ranger” pipeline and outputs a BEDPE file containing the predicted novel adjacencies with corresponding haplotypes, and log-likelihood scores.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

NAIBR

:: MORE INFORMATION

Citation:

Elyanow R, Wu HT, Raphael BJ.
Identifying structural variants using linked-read sequencing data.
Bioinformatics. 2018 Jan 15;34(2):353-360. doi: 10.1093/bioinformatics/btx712. PMID: 29112732; PMCID: PMC5860216.

SNPsnap – Identification and Annotation of matched SNPs

SNPsnap

:: DESCRIPTION

The SNPsnap webserver enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations.

::DEVELOPER

SNPsnap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SNPsnap: a web-based tool for identification and annotation of matched SNPs.
Pers TH, Timshel P, Hirschhorn JN.
Bioinformatics. 2014 Oct 13. pii: btu655.