Tag: Sequence

BCov 1.0 – Predicting Protein beta-sheets from Sequence

BCov 1.0

:: DESCRIPTION

BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence. BCov is based on the PSICOV residue contact predictor, dynamic-programming algorithm for beta-strand alignments and integer programming for beta-sheet topology prediction.

::DEVELOPER

Castrense Savojardo, Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BCov

 :: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 15;29(24):3151-7. doi: 10.1093/bioinformatics/btt555. Epub 2013 Sep 23.
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming.
Savojardo C1, Fariselli P, Martelli PL, Casadio R.

Strelka 2.9.10 – Small Variant Caller

Strelka 2.9.10

:: DESCRIPTION

Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

::DEVELOPER

Illumina, Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX

:: DOWNLOAD

  Strelka

:: MORE INFORMATION

Citation

Kim S, Scheffler K, Halpern AL, Bekritsky MA, Noh E, Källberg M, Chen X, Kim Y, Beyter D, Krusche P, Saunders CT.
Strelka2: fast and accurate calling of germline and somatic variants.
Nat Methods. 2018 Aug;15(8):591-594. doi: 10.1038/s41592-018-0051-x. Epub 2018 Jul 16. PMID: 30013048.

Christopher T. Saunders et al.
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
Bioinformatics (2012) 28 (14): 1811-1817.

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

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