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Taxonomy BLAST Help

The BLAST Taxonomy Reports page (Tax BLAST) presents three different views of the results of a given BLAST run, based on the information inthe NCBI Taxonomy Database. The Tax BLAST reports only include the organisms that are found in the BLAST hitlist.

Organism Report

The simplest report is 'Organism Report'.

This report sorts the BLAST hits according to the species of the target sequence, so that all of the hits to the same organism will appear together. Within each species, the BLAST hits are sorted by score (as for the normal BLAST output). The species themselves are sortedby the strength of their strongest BLAST hit scores.

Each organism entry in the organism report contains a header linewith up to four pieces of information:

 Bombyx mori (domestic silkworm) [moths] taxid 7091 ^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^ ^^^^^ ^^^^^^^^^^ 1 2 3 4
  1. the scientific name of the organism
  2. a vernacular (common) name for the organism, if one is available
  3. the 'blast name'
  4. the 'taxid'
The 'blast name' is a common name for a large group of organisms(e.g. 'mammals' 'flatworms' or 'fungi') that is intended to give ageneral idea of what kind of organism this is, when the scientificname is not familiar.

The 'taxid' is the stable unique identifier for this organismin the NCBI taxonomy database.

note: Some sequence entries may be annotated with names classifiedbelow the species level - these will be treated separately in theTax BLAST reports. For example, there may be entries for both"Homo sapiens" and for "Homo sapiens neandertalensis".

note: If two sequence entries from different species are identical(e.g. EF-1 alpha from human AAA18502 and rabbit CAA27245), only oneof them will appear in the Tax BLAST reports.

note: Some sequence entries do not have source organism information (most patent entries, for example). These will be included in the Tax BLAST reports under the heading "Unresolved taxid".

Lineage Report

The lineage report gives a simplified view of the relationships between the organisms, according to their classification in thetaxonomy database. This report is 'focused' on the organism which yielded the strongest BLAST hit. Note that if the query sequence itself was taken from the database, then the lineage report will be focuses on the organism yielded the strongest BLAST hit.

The lineage report answers the question "how closely are the organisms in the BLAST hitlist related to the query sequence(focus organism) according to the taxonomy database".

The top part of the report shows an abbreviated lineage downto the focus organism:

Fungi/Metazoa group [eukaryotes]. Eumetazoa [animals]. . Bilateria [animals]. . . Coelomata [animals]. . . . Deuterostomia [animals]. . . . . Euteleostomi [vertebrates]. . . . . . Tetrapoda [vertebrates]. . . . . . . Amniota [vertebrates]. . . . . . . . Eutheria [mammals]. . . . . . . . . Homo sapiens (human) ------------------- ...
This list includes the smallest subset of taxonomic groupsthat are required to represent the relationships between theBLAST hitlist organisms and the focus species. The nested vernacular 'blast names' on the right give a rough approximation of therelationships of each species. The first name in the list gives the taxonomic range of the BLAST hitlist organisms - all of the speciesin this list come from the "Fungi/Metazoa group".

The bottom part of the lineage report has a left and a right side.The left side of the report lists the species names (with a commonname, if one is available) nested as they appear within thetaxonomic groups in the top part of the report. Within eachnesting, the species are sorted by the strength of the strongestBLAST hit.

. . . . Deuterostomia [animals]. . . . . Euteleostomi [vertebrates]. . . . . . Tetrapoda [vertebrates]. . . . . . . Amniota [vertebrates]. . . . . . . . Eutheria [mammals]. . . . . . . . . Homo sapiens (human) ------------------- 941 .... . . . . . . . . Cricetulus griseus (Chinese hamster) ... 939 .... . . . . . . . . Mus musculus (house mouse) ............. 939 .... . . . . . . . . Rattus norvegicus (Norway rat) ......... 936 .... . . . . . . . Gallus gallus (chicken) ------------------ 938 .... . . . . . . Xenopus laevis (African clawed frog) ------- 914 .... . . . . . Danio rerio (zebrafish) ---------------------- 872 .... . . . . . Oryzias latipes (Japanese medaka) ............ 833 .... . . . . . Seriola quinqueradiata (five-ray yellowtail) . 823 .... . . . . . Sparus aurata (gilthead sea bream) ........... 820 .... . . . . Anthocidaris crassispina ----------------------- 782 ...
This report focuses on Homo sapiens, the source of the best hit.Cricetulus griseus, Mus musculus and Rattus norvegicus are allplacental mammals (Eutheria) along with Homo sapiens, but none are more closely related to Homo sapiens than thay are to one another.The next most closely related species is the chicken (an amniote), and so on.

The right half of the report gives the BLAST score of the strongest hit from each species (and the title of the correspondingsequence entry) the number of hits, and the 'blast name' associatedwith each of the species.

Taxonomy Report

This report summarizes everything that our classification has to say about the relationships between all of the organisms foundin the BLAST hitlist. The left side of the report gives anabbreviated subset of our classification - only those taxonomicgroups that are required to distinguish each of the organismsfrom all of the rest. The number of blast hits and the numberof species in the hitlist are accumulated up each branch of thetree. This allows you to do a BLAST search with a Drosophilaprotein (for example) and to see how many hits were found inthe Mammalia, or the Archaea, or any taxonomic group that isnot in the Drosophila lineage.

The right side of the report fills in the rest of the lineage (if any) that was not required in the abbreviatedclassification given on the left. This allows you to searchusing browser "Find" menu command for any of the taxonomic groupsfound in the lineageof any of the species in the blast hitlist set. This is oftenuseful delete (for structural reasons) some very well-recognizedtaxa (e.g., Insecta and Mammalia) will not often appear in theabbreviated classifications found in these reports. 'Mammalia',for example will only appear in the abbreviated classificationof these taxonomy reports if the BLAST hitlist includes sequences from one of the monotremes (platypus or echidna)as well as a sequence from one of the other mammals.