dAPE – Annotates Homorepeats (polyX) in Protein Sequence Alignments

dAPE

:: DESCRIPTION

dAPE (dAtabase of Polyx Evolution) helps assessing the evolution of homorepeats and their protein context. It uses by default a weak cutoff (4 out of 6 identical amino acids) to help in the identification of emerging and disappearing homorepeats.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Apr 15;33(8):1221-1223. doi: 10.1093/bioinformatics/btw790.
dAPE: a web server to detect homorepeats and follow their evolution.
Mier P, Andrade-Navarro MA.

CABRA – Cluster & Annotate Blast Results Algorithm

CABRA

:: DESCRIPTION

CABRA is a web tool , which enables a rapid BLAST search in a variety of updated reference proteomes, and provides a new way to functionally evaluate the results by the subsequent clustering of the hits and annotation of the clusters.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

CABRA

:: MORE INFORMATION

Citation

BMC Res Notes. 2016 Apr 30;9:253. doi: 10.1186/s13104-016-2062-y.
CABRA: Cluster and Annotate Blast Results Algorithm.
Mier P, Andrade-Navarro MA.

AutoSequin – automatically Annotate Sequences for Bulk Submission to GenBank

AutoSequin

:: DESCRIPTION

AutoSequin is designed to speed up the process of submitting HIV sequences to GenBank via NCBI’s Sequin program. It is ideal for the batch sequence submission. It makes a special formated table required for running NCBI’s tbl2asn program to generate .sqn file for submission to GenBank.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 AutoSequin

:: MORE INFORMATION

Vcfanno v0.3.2 – Annotate a VCF with other VCFs/BEDs/tabixed files

Vcfanno v0.3.2

:: DESCRIPTION

Vcfanno annotates a VCF with any number of sorted and tabixed input BED, BAM, and VCF files in parallel. It does this by finding overlaps as it streams over the data and applying user-defined operations on the overlapping annotations.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GO

:: DOWNLOAD

Vcfanno

:: MORE INFORMATION

Citation:

Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5.
Vcfanno: fast, flexible annotation of genetic variants.
Pedersen BS, Layer RM, Quinlan AR.

CompAnnotate 1.5 – Annotate base-pairing Interactions in RNA 3D Structures.

CompAnnotate 1.5

:: DESCRIPTION

CompAnnotate is a program for annotation of RNA using comparative method. A better annotation is generated for a low resolution ‘target PDB’ with the help of a high resolution ‘reference PDB’.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CompAnnotate

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2017 Aug 21;45(14):e136. doi: 10.1093/nar/gkx538.
CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.
Islam S, Ge P, Zhang S.

AlignmentComparator 1.1.0 – Visualize and Annotate Differences between Alternative Multiple Sequence Alignments

AlignmentComparator 1.1.0

:: DESCRIPTION

AlignmentComparator is a GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments of the same data set.

::DEVELOPER

BioInfWeb projects,

:: SCREENSHOTS

AlignmentComparator

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

 AlignmentComparator

:: MORE INFORMATION

Citation

Stöver BC, Müller KF:
AlignmentComparator – A GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments.
4th annual Münster Graduate School of Evolution Symposium; Münster, Germany; 2014

vtools 3.0.4 – Annotate, Summarize and Analyze Next-gen Sequencing Variation data

vtools 3.0.4

:: DESCRIPTION

vtools (variant tools) is a set of tools for annotating and tracking sequence variation for large-scale exome sequencing projects. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provide a whole set of tools to manipulate and analyze genetic variants.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C++ compiler
  • Python

:: DOWNLOAD

 vtools

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):421-2. Epub 2011 Dec 2.
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.
San Lucas FA, Wang G, Scheet P, Peng B.

QuasR 1.12.0 – Quantify and Annotate Short Reads in R

QuasR 1.12.0

:: DESCRIPTION

QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification.

::DEVELOPER

Anita Lerch, Dimos Gaiditzis and Michael Stadler <michael.stadler at fmi.ch>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 QuasR

:: MORE INFORMATION

Citaton

QuasR: Quantification and annotation of short reads in R.
Gaidatzis D, Lerch A, Hahne F, Stadler MB.
Bioinformatics. 2014 Nov 21. pii: btu781.

Marky 2.3.0 – Annotate Biomedical Texts using different Annotation Classes

Marky 2.3.0

:: DESCRIPTION

Marky is able to annotate biomedical texts using different annotation classes. You only need a server with php technology and one database to annotate documents with a browser. Users can enter biomedical documents to be annotated by other users and get annotations for relevant terms, such as diseases, symptoms and treatments. Whith Marky you can annote from simple documents (without any formatting) to HTML documents. So that documents can have embedded images and all power of HTML.

::DEVELOPER

SING Group.

:: SCREENSHOTS

Marky

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Apache
  • PHP
  • MySQL 

:: DOWNLOAD

 Marky

:: MORE INFORMATION

Citation

Comput Methods Programs Biomed. 2015 Feb;118(2):242-51. doi: 10.1016/j.cmpb.2014.11.005. Epub 2014 Nov 25.
Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects.
Pérez-Pérez M, Glez-Peña D, Fdez-Riverola F, Lourenço A.

TASR 1.1 – Annotate Transposable Elements using siRNAs Mapping

TASR 1.1

:: DESCRIPTION

TASR (Transposon Annotation using Small RNAs) is a bioinformatic pipeline that can annotate Transposable elements using siRNAs mapping

::DEVELOPER

TASR team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 TASR

:: MORE INFORMATION

Citation

A new approach for annotation of transposable elements using small RNA mapping.
El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA.
Nucleic Acids Res. 2015 Jul 27;43(13):e84. doi: 10.1093/nar/gkv257.