Helpful Links

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Detect Sequence Similarity

Program Location (URL) Purpose
NCBI BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi Detect regions of local similarity between query sequence and sequences in a database
BLAT http://genome.ucsc.edu/cgi-bin/hgBlat Rapid alignment of query sequence against sequences in a genome assembly. Less sensitive than BLAST.
Clustal Omega http://www.ebi.ac.uk/Tools/msa/clustalo/ Generate global alignments of multiple sequences


Web Databases

Program Location (URL) Purpose
UCSC Genome Browser http://genome.ucsc.edu Access to large amount of genome sequence data and annotations
Ensembl http://www.ensembl.org Database containing annotations generated using the Ensembl annotation pipeline. Sequences of genes are available, separated by exons
ExPASy http://us.expasy.org Access to the Swissprot and UniProt databases. Web-based tools for manipulation of sequences.

Gene Predictors

Program Location (URL) Purpose
Genscan http://genes.mit.edu/GENSCAN.html ab initio gene finder (optimized for mammalian genome)


Repeat Finder

Program Location (URL) Purpose
RepeatMasker http://www.repeatmasker.org Find repetitious elements in a query sequence.


Other Useful Programs

Program Location (URL) Purpose
Extractseq http://www.bioinformatics.nl/cgi-bin/emboss/extractseq Extract subsequence from query sequence
Apollo http://genomearchitect.org/ Genome annotation viewer and editor.