Helpful Links

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Detect Sequence Similarity

Program Location (URL) Purpose
NCBI BLAST Detect regions of local similarity between query sequence and sequences in a database
BLAT Rapid alignment of query sequence against sequences in a genome assembly. Less sensitive than BLAST.
Clustal Omega Generate global alignments of multiple sequences

Web Databases

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

Gene Predictors

Program Location (URL) Purpose
Genscan ab initio gene finder (optimized for mammalian genome)

Repeat Finder

Program Location (URL) Purpose
RepeatMasker Find repetitious elements in a query sequence.

Other Useful Programs

Program Location (URL) Purpose
Extractseq Extract subsequence from query sequence
Apollo Genome annotation viewer and editor.