> > Similarity Searching

Similarity Searching

Resources for retrieving sequences similar to your query. Also includes tools for searching for similar sequence profiles.

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Found 46 links

Displaying 15 links

AlgPredTool Content

http://www.imtech.res.in/raghava/algpred/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.

This content is being maintained by raghavagps.

NAR Web Server Issue 2006
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tagsalgorithms allergens amino acid motifs amino acids artificial intelligence epitope mapping epitopes immunoglobulin e proteins

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

BLAST2SRSTool Content

http://blast2srs.embl.de/

Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.

NAR Web Server Issue 2003
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tagsamino acid sequence homology animals humans protein databases

BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html

Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

CHOPTool Content

http://www.rostlab.org/services/CHOP/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence homology protein sequence analysis proteomics tertiary protein structure

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

CrossLinkTool Content

http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.ht...

RNA > Functional RNAs
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.

NAR Web Server Issue 2006
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tagsmicrornas rna sequence analysis sequence alignment

DOUTfinderDatabase Content

http://mendel.imp.ac.at/dout/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Domain Outlier Finder (DOUTfinder) is a tool for facilitating protein domain detection among remotely related protein sequences.

NAR Web Server Issue 2006
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tagsamino acid sequence homology humans tertiary protein structure

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

eBioinformaticsResource Content

http://www.ebioinformatics.org/

DNA > DNA and Genomic Analysis
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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EMBL-EBI FrameworkTool Content

http://www.ebi.ac.uk/Tools/sss

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.

NAR Web Server Issue 2010
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tagscomputational biology nucleic acid databases protein databases sequence alignment sequence analysis

EMBOSSTool Content

http://emboss.bioinformatics.nl/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.

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tagsmolecular biology sequence alignment

FASTA ProgramsTool Content

http://fasta.bioch.virginia.edu/

Sequence Comparison > Similarity Searching

Sequence retrieval and comparison tools.

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tagsadrenergic receptors algorithms amino acid sequence animals antigen receptors base sequence dna eye proteins gene library globins humans information systems molecular sequence data nucleic acid sequence homology peptides proteins rod opsins transforming growth factors

fastSCOPTool Content

http://gemdock.life.nctu.edu.tw/fastSCOP/

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.

NAR Web Server Issue 2007
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tagsamino acid sequence amino acid sequence homology computational biology molecular evolution molecular models molecular sequence data protein conformation protein databases protein sequence analysis protein structural homology proteins statistical data interpretation tertiary protein structure

Tags associated with subcategory 'Sequence Comparison/Similarity Searching'

sequence alignment computational biology protein databases algorithms amino acid sequence homology protein sequence analysis proteins humans amino acid sequence genetic databases animals molecular sequence data protein conformation tertiary protein structure molecular models sequence analysis sensitivity and specificity nucleic acid databases genomics systems integration mice neoplasms multigene family neoplastic gene expression regulation programming languages oligonucleotide array sequence analysis protein structural homology secondary protein structure molecular evolution mamastrovirus proteomics capsid proteins clathrin female genetic promoter regions time factors conserved sequence online systems statistical models normal distribution viral genes viral genome viral proteins University of Manchester biomedical technology assessment equipment failure analysis viral dna gene expression profiling variola virus statistics as topic breast neoplasms caenorhabditis elegans drosophila melanogaster protein folding trna methyltransferases eye proteins gene library dna base sequence nucleotides united states antigen receptors globins information systems peptide library nucleic acids markov chains transforming growth factors nucleic acid sequence homology peptides rod opsins rna sequence analysis reproducibility of results sequence homology computer simulation transcription factors statistical data interpretation rats single nucleotide polymorphism software design consensus sequence dna sequence analysis messenger rna phylogeny protein-serine-threonine kinases genetic models genes evaluation studies as topic factual databases fibronectins vaccinia virus thermoplasma caenorhabditis elegans proteins protein interaction domains and motifs protein interaction mapping glycosyltransferases immunoglobulin e capripoxvirus allergens epitope mapping epitopes