Sequence analysis

The sequence of a linear polymer such as a protein, DNA or RNA is the sequence formed by its monomers. It is also referred to as the primary structure of a given molecule.

The sequence of standard proteins, DNA, or RNA can be expressed as a string over a finite alphabet that represents well-studied monomers. It allows the development of many powerful algorithms and statistics.

Although sequence analysis constitutes an important panel of bioinformatics, sequences are only one of the many forms of experimental data that are available to the bioinformatician.

Protocols

General

• BLAST
• Protein motifs
• Plasmapper
• Wwwblast

Lab-specific protocols

• Wikiomics:BLAST
• Wikiomics:FASTA
• Wikiomics:Multiple sequence alignment
• Wikiomics:Percentage identity
• Wikiomics:Phylogenetic databases
• Wikiomics:Protein function prediction
• Wikiomics:PSI-BLAST
• Wikiomics:RNA gene-finding
• Wikiomics:RNA homology search
• Wikiomics:RNA phylogenetics
• Wikiomics:RNA secondary structure prediction
• Wikiomics:Sequence motifs
• Tregwiki:Collected regulatory elements
• Wikiomics:BLAST tutorial
• Wikiomics:DNA sequencing
• Wikiomics:RNA splicing
• Wikiomics:SAGE
• Wikiomics:Orthologues
• Wikiomics:Mutation/SNP detection

See also

• Wikipedia:Primary structure
• An almost complete list of alignment tools : wikipedia:Sequence alignment software.

Further reading

1. ISBN:0521629713

   subtitle: Probabilistic models of proteins and nucleic acids