SCONE 0.61 – Sequence CONservation Evaluation

SCONE 0.61

:: DESCRIPTION

SCONE (Sequence CONservation Evaluation) reports position-specific measures of conservation.

::DEVELOPER

SUNYAEV LAB

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 SCONE

:: MORE INFORMATION

Citation

Analysis of sequence conservation at nucleotide resolution.
Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S.
PLoS Comput Biol. 2007 Dec;3(12):e254. Epub 2007 Nov 14.

HemeNet – Heme Binding Residue Prediction using Sequence, Structure, and Residue Interaction Network

HemeNet

:: DESCRIPTION

HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2011;6(10):e25560. doi: 10.1371/journal.pone.0025560. Epub 2011 Oct 3.
Computational prediction of heme-binding residues by exploiting residue interaction network.
Liu R1, Hu J.

PhyloMap 2.2.1 – Visualizing Relationships of large Sequence data sets to the influenza A virus genome

PhyloMap 2.2.1

:: DESCRIPTION

The PhyloMap can generate elegant visualizations for large sequence data sets up to thousands of taxon require only a relatively short computation time. It can give you an overview of your entire data set, and automatically select a small number of sequences which are evenly sampled across your data set. You can build a phylogenetic tree using the sampling sequences and use it as a reference data set for further studies. The PhyloMap also shows you the relationships between the sampled data set with the entire data set.

::DEVELOPER

Jiajie Zhang (zhangjiajie@biochem.uni-luebeck.de)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 PhyloMap

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jun 20;12:248. doi: 10.1186/1471-2105-12-248.
PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome.
Zhang J1, Mamlouk AM, Martinetz T, Chang S, Wang J, Hilgenfeld R.

miRseqViewer 1.0 – Visualization of Sequence, Structure and Expression for Analysis of microRNA Sequencing data

miRseqViewer 1.0

:: DESCRIPTION

miRseqViewer is a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multi-panel windows.

::DEVELOPER

miRseqViewer team

:: SCREENSHOTS

miRseqViewer

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Java

:: DOWNLOAD

 miRseqViewer

:: MORE INFORMATION

Citation

miRseqViewer: Multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data.
Jang I, Chang H, Jun Y, Park S, Yang JO, Lee B, Kim W, Kim VN, Lee S.
Bioinformatics. 2014 Oct 15. pii: btu676.

HaploSearch – Haplotype-sequence Two-way Transformation

HaploSearch

:: DESCRIPTION

HaploSearch is a simple tool for transforming DNA sequences into haplotype data and vice versa, speeding up the manipulation of large datasets.

::DEVELOPER

Sergio Delgado Quintero

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

HaploSearch

:: MORE INFORMATION

Citation

Mitochondrion. 2011 Mar;11(2):366-7. doi: 10.1016/j.mito.2010.11.001. Epub 2010 Nov 6.
HaploSearch: a tool for haplotype-sequence two-way transformation.
Fregel R1, Delgado S.

AutoEditor 1.20 – Automated Correction of Genome Sequence Errors

AutoEditor 1.20

:: DESCRIPTION

AutoEditor is a tool for correcting sequencing and basecaller errors using sequence assembly and chromatogram data. On average AutoEditor corrects 80% of erroneous base calls, with an accuracy of 99.99%.This in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AutoEditor

:: MORE INFORMATION

Citation

“Automated correction of genome sequence errors.”
Gajer P, Schatz M, Salzberg SL,
Nucleic Acids Research, 2004. 32(2):562-9.

RefCov 0.3 – Analyzing Coverage of Sequence data across a Reference

RefCov 0.3

:: DESCRIPTION

The RefCov software suite was written as a toolkit to provide multiple methods for analyzing coverage of sequence data across a reference. As such, it does not answer a single question, but rather provides the ability to formulate and answer multiple analytical questions.

::DEVELOPER

The Genome Institute at Washington University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C compiler

:: DOWNLOAD

  RefCov

:: MORE INFORMATION

ProSplign 20170203 – Alignment of Proteins against Genomic Sequences

ProSplign 20170203

:: DESCRIPTION

ProSplign is a global alignment tool developed by Dr. Boris Kiryutin. It produces accurate spliced alignments and locates alignments of distantly related proteins with low similarity.

::DEVELOPER

Dr. Boris Kiryutin (kiryutin@ncbi.nlm.nih.gov)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ProSplign

:: MORE INFORMATION

Citation

ProSplign – Protein to Genomic Alignment Tool.
B. Kiryutin, A. Souvorov, T. Tatusova.
Manuscript in preparation

SDT v1.2 – Sequence Demarcation Tool

SDT v1.2

:: DESCRIPTION

SDT is a free and easy to use program that allows classification of virus sequences based on sequence pairwise identity. It takes as input a FASTA file of aligned or unaligned DNA or protein sequences and aligns every unique pair of sequences, calculates pairwise similarity scores, and displays a colour coded matrix of these scores. It also produces both a plot of these pairwise identity scores and text files containing analysis results.

::DEVELOPER

the University of Cape Town (UCT) Computational Biology (CBIO) Group 

:: SCREENSHOTS

SDTv

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 SDT

:: MORE INFORMATION

Citation:

PLoS One. 2014 Sep 26;9(9):e108277. doi: 10.1371/journal.pone.0108277. eCollection 2014.
SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.
Muhire BM1, Varsani A2, Martin DP

DynaMine Beta – Predicting Protein Dynamics from Sequence

DynaMine Beta

:: DESCRIPTION

DynaMine is a fast predictor of protein backbone dynamics using only sequence information as input.

::DEVELOPER

DynaMine team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DynaMine

:: MORE INFORMATION

Citation

The DynaMine webserver: predicting protein dynamics from sequence.
Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W264-70. doi: 10.1093/nar/gku270