Sole-Search v2 – Peak Detection and Functional Annotation using ChIP-seq data

Sole-Search v2

:: DESCRIPTION

Sole-Search is an integrated peak-calling and analysis softwar which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments.

::DEVELOPER

Korf Lab at the University of California, Davis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Perl

:: DOWNLOAD

 Sole-Search

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jan;38(3):e13. doi: 10.1093/nar/gkp1012. Epub 2009 Nov 11.
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.
Blahnik KR, Dou L, O’Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Lud?scher B, Korf I, Farnham PJ.

Better Bunny 3.0 – Functional Annotation for Rabbit Gene

Better Bunny 3.0

:: DESCRIPTION

Better Bunny is an easy to use tool designed primarily to augment Agilent’s transcriptome-wide rabbit, Oryctolagus cuniculus, gene expression microarray

::DEVELOPER

Dombkowski Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 May 8;13:84. doi: 10.1186/1471-2105-13-84.
Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny.
Craig DB, Kannan S, Dombkowski AA.

mirTools 2.0 – non-coding RNA Discovery, Profiling and Functional Annotation based on High-throughput Sequencing

mirTools 2.0

:: DESCRIPTION

mirTools was developed to allow researchers to comprehensively characterize small RNA transcriptome.

::DEVELOPER

mirTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 mirTools

:: MORE INFORMATION

Citation

Zhu EL, Zhao FQ, Zhou LL, Hou HB, Xu G, Li XK, Bao QY, Sun ZS and Wu JY.
mirTools: microRNA profiling and discovery based on high-throughput sequencing.
Nucl. Acids Res. (2010) 38 (suppl 2): W392-W397.

GenoSkyline 1.2.1 – Tissue-specific Functional Annotation

GenoSkyline 1.2.1

:: DESCRIPTION

GenoSkyline functional annotations is currently available for 9 tissue/cell types. Pre-calculated GS scores for hg19 genome are available for download.

::DEVELOPER

Hongyu Zhao’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 GenoSkyline

:: MORE INFORMATION

Citation

Lu Q.*, Powles R.*, Wang Q., He B., and Zhao H.
Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome wide association studies. (Submitted)

Dintor – Functional Annotation of Genomic and Proteomic data

Dintor

:: DESCRIPTION

Dintor is a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets.

::DEVELOPER

the Center of Biomedicine (CBM)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Dintor

:: MORE INFORMATION

Citation

Dintor: functional annotation of genomic and proteomic data.
Weichenberger CX, Blankenburg H, Palermo A, D’Elia Y, K?nig E, Bernstein E, Domingues FS.
BMC Genomics. 2015 Dec 21;16(1):1081. doi: 10.1186/s12864-015-2279-5.

PANNZER2 – Protein Functional Annotation Server

PANNZER2

:: DESCRIPTION

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE), EC numbers and GO classes.

::DEVELOPER

Liisa Holm’s Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • MySQL
  • Blast

:: DOWNLOAD

 PANNZER2

:: MORE INFORMATION

Citation

Törönen P, Medlar A, Holm L.
PANNZER2: a rapid functional annotation web server.
Nucleic Acids Res. 2018 Jul 2;46(W1):W84-W88. doi: 10.1093/nar/gky350. PMID: 29741643; PMCID: PMC6031051.

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.
Koskinen P, Törönen P, Nokso-Koivisto J, Holm L.
Bioinformatics. 2015 Jan 8. pii: btu851

FINDSITE 1.0 – Ligand-binding Site Prediction & Functional Annotation

FINDSITE 1.0

:: DESCRIPTION

FINDSITE is a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FINDSITE

:: MORE INFORMATION

Citation

Skolnick J and Brylinski M (2009)
FINDSITE: a combined evolution/structure-based approach to protein function prediction.
Brief Bioinform 10:378-91

SNPnexus v4 – Functional Annotation of novel and publicly known Genetic Variants

SNPnexus V4

:: DESCRIPTION

SNPnexus was designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms (SNP) for large-scale genotyping studies of multifactorial disorders.

::DEVELOPER

Cancer Bioinformatics Group at the Barts Cancer Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W65-70. doi: 10.1093/nar/gks364.
SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update).
Dayem Ullah AZ, Lemoine NR, Chelala C.

Argot2 – Functional Annotation of Proteins using the Semantic Similarity in the Gene Ontology

Argot2

:: DESCRIPTION

Argot2 (Annotation Retrieval of Genel Ontology Terms) is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate.

::DEVELOPER

Argot2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S14. doi: 10.1186/1471-2105-13-S4-S14.
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
Falda M1, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P.

ANNOVAR 20210202 – functional ANNOtation of genetic VARiants

ANNOVAR 20210202

:: DESCRIPTION

ANNOVAR (ANNOtation of genetic VARiants) is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides

::DEVELOPER

ANNOVAR Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ANNOVAR

:: MORE INFORMATION

Citation:

Wang K, Li M, Hakonarson H.
ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data
Nucleic Acids Research, 38:e164, 2010