[Genome] Hello UCSC Genome browser staff

[Brooke Rhead]

Hello Erez,

Thank you for the compliments on the browser.  I will answer each of 
your questions below.

1. Is there a textual output for the browser? parsing is much easier 
from text than from graphical displays.

- Yes, please see our downloads page at 
http://hgdownload.cse.ucsc.edu/downloads.html .  All of our tables are 
available as compressed text files.  The tables that underlie the Genome 
Browser tracks are under the "Annotation database" link.

2. If my sequence falls within a gene, on what (number) exon/intron does 
it fall?

- Note that there are several different gene tracks under the "Genes and 
Gene Prediction Tracks" section, based on data from different sources. 
You can read about each track by clicking the name of the track in the 
Genome Browser (the blue link above the track control) to determine 
which gene track suits your purposes best.  You can also see the format 
of table by clicking the "View table schema" link on this page.

The gene tables all have the same basic format, which includes the 
number of exons ('exonCount'), the exon start positions ('exonStarts'), 
and exon end positions ('exonEnds').  There is also a 'strand' field 
that indicates whether the gene is on the + or - strand.  Genes on the + 
strand are displayed 5' to 3' in the Genome Browser, and the first exon 
in the gene will be the one with the lowest genome coordinate.  Genes on 
the - strand are displayed 3' to 5' in the Genome Browser, and the first 
exon in the gene is the one with the highest genome coordinate.

3. What is the directionality of the adjacent gene/s to my sequence?

- This is indicated by the 'strand' field, described in the previous answer.

4. If my sequence falls within a repeat, how do I know on which type of
repeat: LINE, SINE or LTR.

- The RepeatMasker track indicates the repeat type.  The table for this 
track is 'rmsk'.  Look for the 'repClass' field.  Note that this table 
is actually broken up into smaller tables for each chromosome due to its 
large size.

I hope this information is helpful to you.  If you have further 
questions or if we can clarify any of the answers above, please do not 
hesitate to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



ארז ליבנה wrote:
> Hello UCSC Genome browser staff,
> 
> First of all,
> thank you for the excellent genome browser, it is very useful.
> 
> I am involved in a mouse genome research and wish to analyse a large
> quantity of DNA sequences automatically based on you browser. To this aim, I
> am composing a software that parses information from USCS browser to a
> spreadsheet.
> I have a few questions:
> 
> 1. Is there a textual output for the browser? parsing is much easier from
> text than from graphical displays.
> 
> Also,
> I am having difficulties getting some of the information textually:
> 
> 2. If my sequence falls within a gene, on what (number) exon/intron does it
> fall?
> 
> 3. What is the directionality of the adjacent gene/s to my sequence?
> 
> 4. If my sequence falls within a repeat, how do I know on which type of
> repeat: LINE, SINE or LTR.
> 
> 
> Thank you in advance,
> Erez Livneh
> Hebrew University
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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