Database Search Only
| Name | Description | Sequence Type* | Link | Authors | Year |
|---|---|---|---|---|---|
| BLAST | local search with fast k-tuple heuristic (Basic Local Alignment Search Tool) | Both | NCBI EBI DDBJ DDBJ (psi-blast) GenomeNet PIR (protein only) | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ | 1990 |
| CS-BLAST | sequence-context specific BLAST, more sensitive than BLAST, FASTA, and SSEARCH. Position-specific iterative version CSI-BLAST more sensitive than PSI-BLAST | Protein | CS-BLAST server download | Angermueller C, Biegert A, Soeding J | 2013 |
| CUDASW++ | GPU accelerated Smith Waterman algorithm for multiple shared-host GPUs | Protein | homepage publication | Liu Y, Maskell DL and Schmidt B | 2009/2010 |
| FASTA | local search with fast k-tuple heuristic, slower but more sensitive than BLAST | Both | EBI DDBJ GenomeNet PIR (protein only) | ||
| GGSEARCH / GLSEARCH | Global:Global (GG), Global:Local (GL) alignment with statistics | Protein | FASTA server | ||
| HMMER | local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST | Both | download | Durbin R, Eddy SR, Krogh A, Mitchison G | 1998 |
| HHpred / HHsearch | pairwise comparison of profile Hidden Markov models; very sensitive, but can only search alignment databases (Pfam, PDB, InterPro...) | Protein | server download | Söding J | 2005 |
| IDF | Inverse Document Frequency | Both | download | ||
| Infernal | profile SCFG search | RNA | download | Eddy S | |
| PSI-BLAST | position-specific iterative BLAST, local search with position-specific scoring matrices, much more sensitive than BLAST | Protein | NCBI PSI-BLAST | Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ | 1997 |
| PSI-Search | Combining the Smith-Waterman search algorithm with the PSI-BLAST profile construction strategy to find distantly related protein sequences, and preventing homologous over-extension errors. | Protein | EBI PSI-Search | Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR | 2012 |
| ScalaBLAST | Highly parallel Scalable BLAST | Both | ScalaBLAST | Oehmen et al. | 2011 |
| Sequilab | Linking and profiling sequence alignment data from NCBI-BLAST results with major sequence analysis servers/services | Nucleotide/peptide | server | 2010 | |
| SAM | local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST | Both | SAM | Karplus K, Krogh A | 1999 |
| SSEARCH | Smith-Waterman search, slower but more sensitive than FASTA | Both | EBI DDBJ | ||
Read more about this topic: List Of Sequence Alignment Software
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—Ralph Waldo Emerson (1803–1882)