Structure and Sequence Feature Detection

This section contains links to tools for DNA structure prediction and finding regulatory sequences, the base composition, binding sites and motifs in your sequence of interest.

Found 162 links

Displaying 15 links

3D-DARTTool Content

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The 3D-DART web server interfaces to a collection of tools for the generation of DNA structural models in custom conformations.

This content is being maintained by mvdijk.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
3D-DART: a DNA structure modelling server200918

ALGGENTool Content

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ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

AlignACETool Content

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Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement.

links directory index: not available
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AUGUSTUSTool Content

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AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

BEARRTool Content

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Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

BiDaSTool Content

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BiDaS is a web-server that can massively generate Monte Carlo simulated sequences and numerical feature data sets.

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Bioinformatics ToolkitTool Content

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This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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n/a

bioNMFTool Content

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A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

BWT-SWTool Content

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BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments (see BLAST Sensitivity), BWT-SW finds all local alignments.

links directory index: 47
TitlePublication YearGoogle Scholar Citation Count
Compressed indexing and local alignment of DNA200847

CEASTool Content

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Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
CEAS: cis-regulatory element annotation system200673

CGView ServerTool Content

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The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

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