Similarity Searching and Classification

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

Found 56 links

Displaying 15 links

aLeavesTool Content

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aLeaves web server supports homolog collection from diverse animal genomes. An input sequence is passed through the server to collect similar sequences for molecular phylogenetic analysis.

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BLASTTool Content

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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. A new BLAST report allows faster loading of alignments, has navigation aids and has improved usability.

BLAST2SRSTool Content

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

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

CHOPTool Content

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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.

links directory index: 32
TitlePublication YearGoogle Scholar Citation Count
CHOP: parsing proteins into structural domains200432

CMCompareTool Content

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CMCompare wbe server uses covariance models to compare infernal RNA family models to identify models with poor specificity and explore the relationship between models.

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ConoDictorTool Content

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The ConoDictor tool enables fast and accurate classification of conopeptides (the main bioactive component of cone snail venom) into superfamilies based on their amino acid sequence. Predictions are made using Hidden Markov Models and generalized profiles.

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CrossLinkTool Content

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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.

eBioinformaticsResource Content

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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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