PageMan 0.12 – Annotates, Investigates, and Condenses Microarray data in the Context of Functional Ontologies

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

:: 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

:: 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.

MyRAST r45 – Annotate Genome

MyRAST r45

:: DESCRIPTION

MyRAST (Rapid Annotations using Subsystems Technology) is a software for the RAST Server, a fully automated annotation service for complete, or near-complete, archaeal and bacterial genomes.

::DEVELOPER

The SEED framework for comparative genomics

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Linux / Windows

:: DOWNLOAD

MyRAST

:: MORE INFORMATION

Citation:

Ramy K Aziz, etc.
The RAST Server: Rapid Annotations using Subsystems Technology
BMC Genomics. 2008; 9: 75.

SAS – Sequence Annotated by Structure

SAS

:: DESCRIPTION

SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank (PDB). The resultant multiple alignment can be coloured according to different structural features and the matching 3D structures can be superimposed and viewed in RasMol.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Protein Eng. 1998 Oct;11(10):855-9.
Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
Milburn D, Laskowski RA, Thornton JM.