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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 in the 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 sorted by the strength of their strongest BLAST hit scores.

Each organism entry in the organism report contains a header line with 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 a general idea of what kind of organism this is, when the scientific name is not familiar.

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

note: Some sequence entries may be annotated with names classified below the species level - these will be treated separately in the Tax 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 one of 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 the taxonomy 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 down to 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 groups that are required to represent the relationships between the BLAST hitlist organisms and the focus species. The nested vernacular 'blast names' on the right give a rough approximation of the relationships of each species. The first name in the list gives the taxonomic range of the BLAST hitlist organisms - all of the species in 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 common name, if one is available) nested as they appear within the taxonomic groups in the top part of the report. Within each nesting, the species are sorted by the strength of the strongest BLAST 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 all placental 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 corresponding sequence entry) the number of hits, and the 'blast name' associated with each of the species.

Taxonomy Report

This report summarizes everything that our classification has to say about the relationships between all of the organisms found in the BLAST hitlist. The left side of the report gives an abbreviated subset of our classification - only those taxonomic groups that are required to distinguish each of the organisms from all of the rest. The number of blast hits and the number of species in the hitlist are accumulated up each branch of the tree. This allows you to do a BLAST search with a Drosophila protein (for example) and to see how many hits were found in the Mammalia, or the Archaea, or any taxonomic group that is not 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 abbreviated classification given on the left. This allows you to search using browser "Find" menu command for any of the taxonomic groups found in the lineage of any of the species in the blast hitlist set. This is often useful delete (for structural reasons) some very well-recognized taxa (e.g., Insecta and Mammalia) will not often appear in the abbreviated classifications found in these reports. 'Mammalia', for example will only appear in the abbreviated classification of 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.