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<CENTER><H2>Taxonomy BLAST Help</H2></CENTER>
<HR>
The BLAST Taxonomy Reports page (Tax BLAST) presents three different
views of the results of a given BLAST run, based on the information in
<a href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html">the NCBI Taxonomy Database.</a> The Tax BLAST reports only include the organisms that
are found in the BLAST hitlist.
<h3>Organism Report</h3>
The simplest report is 'Organism Report'.
<P>
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.
<P>
Each organism entry in the organism report contains a header line
with up to four pieces of information:
<PRE>
Bombyx mori (domestic silkworm) [moths] taxid 7091
^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^ ^^^^^ ^^^^^^^^^^
1 2 3 4
</PRE>
<OL>
<LI>the scientific name of the organism
<LI>a vernacular (common) name for the organism, if one is available
<LI>the 'blast name'
<LI>the 'taxid'
</OL>
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.
<P>
The 'taxid' is the stable unique identifier for this organism
in the NCBI taxonomy database.
<P>
<b><i>note:</i></b> 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".
<P>
<b><i>note:</i></b> 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.
<P>
<b><i>note:</i></b> 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".
<h3>Lineage Report</h3>
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.
<P>
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".
<P>
The top part of the report shows an abbreviated lineage down
to the focus organism:
<PRE>
Fungi/Metazoa group [eukaryotes]
. Eumetazoa [animals]
. . Bilateria [animals]
. . . Coelomata [animals]
. . . . Deuterostomia [animals]
. . . . . Euteleostomi [vertebrates]
. . . . . . Tetrapoda [vertebrates]
. . . . . . . Amniota [vertebrates]
. . . . . . . . Eutheria [mammals]
. . . . . . . . . Homo sapiens (human) ------------------- ...
</PRE>
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".
<P>
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.
<PRE>
. . . . 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 ...
</PRE>
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.
<P>
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.
<h3>Taxonomy Report</h3>
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.
<P>
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.