Homology search
3 methods · 2001–2009
Homology search: De novo sequences, errors and all, used as the query in an error-tolerant search against known proteins, so a protein that is in no database can still be identified through its relatives.
De novo sequences, errors and all, used as the query in an error-tolerant search against known proteins, so a protein that is in no database can still be identified through its relatives.
The earliest of its 3 methods is MS BLAST (2001); 2 more have followed.
| Methods | 3 |
| Papers describing them | 4 |
| Authors | 18 |
| Active | 2001-05-01 to 2009-09-01 |
| Kinds | adjacent (3) |
| Acquisition | DDA (3) |
Methods (3)
Oldest first, by the paper that describes each one.
- MS BLAST (2001): Homology search of error-tolerant de novo sequences against a protein database, introduced for charting the proteomes of organisms with unsequenced genomes and later used to validate borderline identifications.
- SPIDER (2005): Protein identification from sequence tags while accounting for de novo sequencing error.
- Champs (2009): Sequences a complete novel protein by de novo sequencing its peptides and then assembling them against a HOMOLOGOUS database rather than an exact one, reaching near-full coverage and accuracy where neither approach alone would.
Papers describing them (4)
- Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching (2001, Analytical Chemistry, peer-reviewed)
- SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005, Journal of Bioinformatics and Computational Biology, peer-reviewed)
- Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches (2006, Journal of Proteome Research, peer-reviewed)
- Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy (2009, Bioinformatics, peer-reviewed)