RoundUp: Difference between revisions
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== User notes == | == User notes == | ||
A common procedure for identifying sequence pairs that are putatively orthologous is the Reciprocal Best Hit (RBH) approach - usually using Blast hits. Protein '''''i''''' in genome '''I''' is a RBH of protein '''''j''''' in genome '''J''' if query of genome '''J''' with protein '''''i''''' yields as the top hit protein '''''j''''', and reciprocal query of genome '''I''' with protein '''''j''''' yields at the top hit protein '''''i'''''. However, the highest scoring hit need not be the nearest phylogenetic neighbor of the query sequence. If the forward blast yields a paralogous best hit but the reciprocal blast recovers an actual ortholog, both pairs will be '''excluded'''. Thus, RBH will rightfully prevent admission of the paralogous pair to the set of proteins for which relative evolutionary rates are estimated, it will also wrongly exclude an orthologous pair. | |||
Reciprocal Smallest Distance (RSD) relies on global sequence alignment and maximum likelihood estimation of evolutionary distances to detect orthologs between two genomes. RSD preserves the safeguard of reciprocal genome queries, but is less vulnerable to exclusion of orthologs due to identification of a paralog in one blast direction. | |||
Roundup is a tool for ortholog and phylogenetic profile retrieval Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the RSD algorithm. Some salient features about the RoundUp Web-Search Tool: | |||
* it uses four increasingly stringent blast E-value thresholds 1e-5, 1e-10,1e-15 and 1e-20, and three increasingly stringent divergence thresholds, 0.8, 0.5 and 0.2 | |||
* for every pair of genomes, 12 possibly different sets of orthologs exist | |||
The [https://rodeo.med.harvard.edu/tools/roundup/index.php?action=input_browse Roundup web-search tool] requires these parameters as input: | |||
* primary genome | |||
* one or more secondary genomes | |||
* divergence cutoff | |||
* Blast Evalue cutoff | |||
If the 2 genomes being compared are very close in evolutionary distance, one would use a very stringent divergence cut-off (0.2) and a very stringent Blast EValue cut-off (1E-20). | |||
== See Also == | == See Also == | ||
Revision as of 07:56, 9 October 2007
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A common procedure for identifying sequence pairs that are putatively orthologous is the Reciprocal Best Hit (RBH) approach - usually using Blast hits. Protein i in genome I is a RBH of protein j in genome J if query of genome J with protein i yields as the top hit protein j, and reciprocal query of genome I with protein j yields at the top hit protein i. However, the highest scoring hit need not be the nearest phylogenetic neighbor of the query sequence. If the forward blast yields a paralogous best hit but the reciprocal blast recovers an actual ortholog, both pairs will be excluded. Thus, RBH will rightfully prevent admission of the paralogous pair to the set of proteins for which relative evolutionary rates are estimated, it will also wrongly exclude an orthologous pair.
Reciprocal Smallest Distance (RSD) relies on global sequence alignment and maximum likelihood estimation of evolutionary distances to detect orthologs between two genomes. RSD preserves the safeguard of reciprocal genome queries, but is less vulnerable to exclusion of orthologs due to identification of a paralog in one blast direction.
Roundup is a tool for ortholog and phylogenetic profile retrieval Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the RSD algorithm. Some salient features about the RoundUp Web-Search Tool:
- it uses four increasingly stringent blast E-value thresholds 1e-5, 1e-10,1e-15 and 1e-20, and three increasingly stringent divergence thresholds, 0.8, 0.5 and 0.2
- for every pair of genomes, 12 possibly different sets of orthologs exist
The Roundup web-search tool requires these parameters as input:
- primary genome
- one or more secondary genomes
- divergence cutoff
- Blast Evalue cutoff
If the 2 genomes being compared are very close in evolutionary distance, one would use a very stringent divergence cut-off (0.2) and a very stringent Blast EValue cut-off (1E-20).
See Also
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