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The purpose of the Assembly vs. BAC
End Pairs pages is to compare the clone positioning on
each map for each chromosome against available BAC end pairs
data from the dbGSS
database at NCBI. Each of the BAC end sequences are placed on
the assembled draft sequence and the individual accessioned
clones which are available for a particular GenBank freeze.
Phase 0 sequences in the freeze are not considered. The BAC
end sequence placement is done using Jim Kent's BLAT program.
It should be noted that the BAC end data is very noisy with
estimates of 15% error, and therefore should be used with
caution. Generally, it is best to have at least two separate
pairs confirming a link between regions before any conclusions
can be drawn. It is best to also use this data in conjunction
with other data available.
The placements of valid BAC end pairs on the assembled draft
sequence can also be seen in the corresponding freeze version
of the UCSC
Human Genome Browser under the BAC End Pairs track.
The BAC End Pairs pages report the results of these placements
in tables with the following columns:
- Links - links to other pages with information for this accession - Summary(S),
Genetic(G), YAC(Y), RH(R), BAC End Pairs(B), Overlaps(O)
- Contig1 - name of contig in which one BAC end is placed
- Acc1 - GenBank accession of clone in which one BAC end is placed.
- Start1 - base pair in chromosome where BAC end sequence starts.
- Phs - phase of Acc1 sequence in freeze.
- BAC End Acc1 - GenBank accession of one BAC end sequence
- Or1 - Orientation of BAC end sequence on the assembled sequence
- Chr2 - chromosome in which the other BAC end is placed
- Contig2 - name of contig in which other BAC end is placed
- Acc2 - GenBank accession of clone in which other BAC end is placed. Clicking
on this will cause the contig with that accession to be displayed
- Start2 - base pair in chromosome where BAC end sequence starts.
- Phs - phase of Acc2 sequence in freeze.
- BAC End Acc2 - GenBank accession of other BAC end sequence.
- Or2 - Orientation of other BAC end sequence on the assembled sequence
- Clone - name of clone which BAC end sequences come from. On white lines,
this summarizes the number of confirming BAC end pairs for this accession
There are separate tables for each of the contigs in a
chromosome. Each accession in a contig begins with a white
colored line which reports the number of "confirming" BAC end
pairs. By this we mean that the second BAC end sequence is
placed in an accessioned clone which is also located in this
contig no more than 1Mb away, thus it is "close". This would
provide evidence that both clones belong in this contig.
These pairs are not listed in the main table to save space,
but by clicking on the link in the last cell ("# confirm"), a
second window will appear displaying the confirming BAC end
pairs for the whole contig with the desired accession at or
near the top.
In addition to the white colored lines, there are also other
colored lines for other BAC end pair combinations in which one
BAC end sequence is placed in this accessioned clone. The
following are the interpretations of each of the different
colors:
- Blue - the second BAC end pair hits an accessioned
clone no more than 1Mb away located in a contig immediately
adjacent to this contig. These indicate that the clone
associated with the BAC end pair may span this gap.
- Green - the second BAC end pair hits an accessioned
clone no more than 1Mb away located in a contig that is two
or three contigs removed from this contig. These are
identified due to the chance that small contigs may be
inserted in between the two BAC ends, but this clone may
still span this area.
- Pink - the second BAC end pair hits an accessioned
clone located in a contig that is still on this chromosome,
but at a distance of more than 1Mb.
- Red - the second BAC end pair hits an accessioned clone
located in a contig that is on a different chromosome.
For the Pink and Red colored BAC ends, there is an additional
requirement that a second BAC end pair also supports linking the
two regions. This is calculated by assigning each end to a 3Mb
region in the draft sequence, and determining if another BAC end
pair links these two regions.
The coloring is provided to help verify the placements of
clones in the draft sequence, and also to suggest areas in
which two clones that should be closer together in the
sequence have been separated. Red and Pink colored lines
should not be interpreted as there is necessarily a mistake
with the accession being viewed, but that a second accession
that may actually be close has been placed at a
distance.
The pages are designed so that you can view one contig at a
time, or all contigs for a single chromosome at once. A
header frame is provided on each page to allow for easier
navigation through the table, to provide a reference for the
meanings of the line colors, and to display the table column
names for convenience when viewing longer contigs.
Warning: Many of the pages contain very large tables
and may take a while to load, especially for the larger
chromosomes. Please be patient.
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