Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss?
Reciprocal Best Hits (RBH) are a common proxy for orthology in comparative genomics. Essentially, a RBH is found when the proteins encoded by two genes, each in a different genome, find each other as the best scoring match in the other genome. NCBI's BLAST is the software most usually used for...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4094424?pdf=render |
| _version_ | 1818192268491751424 |
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| author | Natalie Ward Gabriel Moreno-Hagelsieb |
| author_facet | Natalie Ward Gabriel Moreno-Hagelsieb |
| author_sort | Natalie Ward |
| collection | DOAJ |
| description | Reciprocal Best Hits (RBH) are a common proxy for orthology in comparative genomics. Essentially, a RBH is found when the proteins encoded by two genes, each in a different genome, find each other as the best scoring match in the other genome. NCBI's BLAST is the software most usually used for the sequence comparisons necessary to finding RBHs. Since sequence comparison can be time consuming, we decided to compare the number and quality of RBHs detected using algorithms that run in a fraction of the time as BLAST. We tested BLAT, LAST and UBLAST. All three programs ran in a hundredth to a 25th of the time required to run BLAST. A reduction in the number of homologs and RBHs found by the faster algorithms compared to BLAST becomes apparent as the genomes compared become more dissimilar, with BLAT, a program optimized for quickly finding very similar sequences, missing both the most homologs and the most RBHs. Though LAST produced the closest number of homologs and RBH to those produced with BLAST, UBLAST was very close, with either program producing between 0.6 and 0.8 of the RBHs as BLAST between dissimilar genomes, while in more similar genomes the differences were barely apparent. UBLAST ran faster than LAST, making it the best option among the programs tested. |
| first_indexed | 2024-12-12T00:27:48Z |
| format | Article |
| id | doaj.art-c6a41d44632c49f9925cd0a5f25155e2 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T00:27:48Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c6a41d44632c49f9925cd0a5f25155e22022-12-22T00:44:34ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0197e10185010.1371/journal.pone.0101850Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss?Natalie WardGabriel Moreno-HagelsiebReciprocal Best Hits (RBH) are a common proxy for orthology in comparative genomics. Essentially, a RBH is found when the proteins encoded by two genes, each in a different genome, find each other as the best scoring match in the other genome. NCBI's BLAST is the software most usually used for the sequence comparisons necessary to finding RBHs. Since sequence comparison can be time consuming, we decided to compare the number and quality of RBHs detected using algorithms that run in a fraction of the time as BLAST. We tested BLAT, LAST and UBLAST. All three programs ran in a hundredth to a 25th of the time required to run BLAST. A reduction in the number of homologs and RBHs found by the faster algorithms compared to BLAST becomes apparent as the genomes compared become more dissimilar, with BLAT, a program optimized for quickly finding very similar sequences, missing both the most homologs and the most RBHs. Though LAST produced the closest number of homologs and RBH to those produced with BLAST, UBLAST was very close, with either program producing between 0.6 and 0.8 of the RBHs as BLAST between dissimilar genomes, while in more similar genomes the differences were barely apparent. UBLAST ran faster than LAST, making it the best option among the programs tested.http://europepmc.org/articles/PMC4094424?pdf=render |
| spellingShingle | Natalie Ward Gabriel Moreno-Hagelsieb Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PLoS ONE |
| title | Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? |
| title_full | Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? |
| title_fullStr | Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? |
| title_full_unstemmed | Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? |
| title_short | Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? |
| title_sort | quickly finding orthologs as reciprocal best hits with blat last and ublast how much do we miss |
| url | http://europepmc.org/articles/PMC4094424?pdf=render |
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