> > Analysis of Aligned Sequences

Analysis of Aligned Sequences

Resources for the interpretation of the results of comparing sets of sequences. Includes tools for functional inference from multispecies comparisons.

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AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/

DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

NAR Web Server Issue 2004
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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

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.

NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/

Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

NAR Web Server Issue 2004
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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

Blocks WWW ServerTool Content

http://blocks.fhcrc.org/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.

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tagsadenosine triphosphatases algorithms amino acid sequence amino acid sequence homology animals computational biology dna helicases dna-binding proteins factual databases humans molecular sequence data nuclear proteins proteins sequence alignment software design transcription factors

CAMPOTool Content

http://schubert.bio.uniroma1.it/CAMPO/index.html

Sequence Comparison > Analysis of Aligned Sequences

CAMPO is a tool to analyze conserved regions from a multiple sequence alignment

NAR Web Server Issue 2005
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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

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.

NAR Web Server Issue 2008
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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

CHC_FINDTool Content

http://schubert.bio.uniroma1.it/CHC_FIND/index.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Sequence Comparison > Analysis of Aligned Sequences

CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

NAR Web Server Issue 2005
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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

ClanToxTool Content

http://www.clantox.cs.huji.ac.il

Sequence Comparison > Analysis of Aligned Sequences

ClanTox, a classifier of short animal toxins, predicts whether input sequences are toxin-like based on classification system training to known animal toxins. This dscovery prediction tool also outputs presence of signal peptide, the number of cysteine residues and the associated functional annotations.

NAR Web Server Issue 2009
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tagsanimals biological toxins cysteine protein sequence analysis proteomics

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

ConSurfTool Content

http://consurf.tau.ac.il/

Protein > 3-D Structural Features
Sequence Comparison > Analysis of Aligned Sequences

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsamino acid sequence amino acid sequence homology amino acid substitution amino acids bacterial proteins base sequence bayes theorem bcl-x protein conserved sequence molecular evolution molecular models nucleic acid conformation phylogeny potassium channels protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins c-bcl-2 sequence alignment sequence analysis

CorreLogoTool Content

http://correlogo.abcc.ncifcrf.gov/

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.

NAR Web Server Issue 2006
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tagsdna sequence analysis nucleic acid conformation ribosomal rna rna sequence analysis sequence alignment transfer rna

CRASPTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/

Sequence Comparison > Analysis of Aligned Sequences

Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.

NAR Web Server Issue 2004
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tagsamino acid substitution protein sequence analysis sequence alignment

CSTminerTool Content

http://www.caspur.it/CSTminer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences

CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.

NAR Web Server Issue 2004
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tagsanimals conserved sequence exons genomics humans intergenic dna mice nucleic acid regulatory sequences sequence tagged sites

ECR BrowserTool Content

http://ecrbrowser.dcode.org/

Model Organisms > Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

NAR Web Server Issue 2004
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tagsanimals binding sites dna sequence analysis fishes genome genomics humans mice nucleic acid regulatory sequences rats sequence alignment synteny systems integration transcription factors

Tags associated with subcategory 'Sequence Comparison/Analysis of Aligned Sequences'

sequence alignment computational biology proteins algorithms animals protein sequence analysis humans molecular sequence data phylogeny conserved sequence genomics amino acid sequence dna sequence analysis molecular evolution molecular models protein conformation amino acid sequence homology protein databases base sequence mice binding sites tertiary protein structure bacterial genome quantitative structure-activity relationship amino acids fungal genome plant genome escherichia coli proteins bacterial proteins bacterial genes caenorhabditis elegans escherichia coli horses helminth genes database management systems trypsin inhibitors viral matrix proteins open reading frames drosophila nucleic acid databases genetic polymorphism trna methyltransferases polymerase chain reaction synteny systems integration expressed sequence tags protein folding artificial intelligence fishes terminology as topic intergenic dna peptides invertebrates sequence homology plants bayes theorem genetic databases mamastrovirus protein structural homology secondary protein structure statistics as topic statistical data interpretation proto-oncogene proteins clathrin likelihood functions markov chains src homology domains capsid proteins statistical models genetic models protozoan genes pan troglodytes papio rabbits rats nucleic acid sequence homology nucleic acid repetitive sequences human genome kinesin leukemia nucleic acid regulatory sequences reproducibility of results sensitivity and specificity dna-binding proteins factual databases nuclear proteins software design dna helicases zebrafish single nucleotide polymorphism swine takifugu untranslated regions time factors human chromosomes genome succinate dehydrogenase messenger rna protein-serine-threonine kinases rna sequence analysis genes