FeatureScan: Revealing Property-dependent Similarity of Nucleotide Sequences

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Jul 18

PMID 16845077

Citations 9

Authors

Igor V Deyneko

Bjorn Bredohl

Daniel Wesely

Yulia M Kalybaeva

Alexander E Kel

Helmut Blocker

Gerhard Kauer

Affiliations

Soon will be listed here.

Abstract

FeatureScan is a software package aiming to reveal novel types of DNA sequence similarity by comparing physico-chemical properties. Thirty-eight different parameters of DNA double strands such as charge, melting enthalpy, conformational parameters and the like are provided. As input FeatureScan requires two sequences, a pattern sequence and a target sequence, search conditions are set by selecting a specific DNA parameter and a threshold value. Search results are displayed in FASTA format and directly linked to external genome databases/browsers (ENSEMBL, NCBI, UCSC). An Internet version of FeatureScan is accessible at http://genome.gbf.de/featurescan/. As part of the HOBIT initiative (http://hobit.sourceforge.net/) FeatureScan is also accessible as a web service at its above home page. Currently, several preloaded genomes are provided at this Internet website (Homo sapiens, Mus musculus, Rattus norvegicus and four strains of Escherichia coli) as target sequences. Standalone executables of FeatureScan are available on request.

Citing Articles

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Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters.

Chadaeva I, Ponomarenko P, Rasskazov D, Sharypova E, Kashina E, Zhechev D BMC Genomics. 2018; 19(Suppl 3).

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FlowerMorphology: fully automatic flower morphometry software.

Rozov S, Deineko E, Deyneko I Planta. 2018; 247(5):1163-1173.

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Candidate SNP markers of aggressiveness-related complications and comorbidities of genetic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters.

Chadaeva I, Ponomarenko M, Rasskazov D, Sharypova E, Kashina E, Matveeva M BMC Genomics. 2017; 17(Suppl 14):995.

PMID: 28105927 PMC: 5249025. DOI: 10.1186/s12864-016-3353-3.

Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.

Ponomarenko P, Rasskazov D, Suslov V, Sharypova E, Savinkova L, Podkolodnaya O Biomed Res Int. 2016; 2016:8642703.

PMID: 27635400 PMC: 5011241. DOI: 10.1155/2016/8642703.

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