UCSC Archaeal genome

browserAdvanced browsing

UCSC Archaeal genome

browserAdvanced browsing

September 19, 2006David Bernick, Aaron Cozen and Todd Lowe

September 19, 2006David Bernick, Aaron Cozen and Todd Lowe

AgendaAgenda

Basic searches with the Archaea Genome browser Text searches Sequence searching - BLAT, short sequences In-silico PCR Hands-on session - Navigation and searching

Advanced features Table Browser Custom tracks Conservation tracks and inter-species navigation Hands-on session - Table Browser and Custom tracks

Basic searches with the Archaea Genome browser Text searches Sequence searching - BLAT, short sequences In-silico PCR Hands-on session - Navigation and searching

Advanced features Table Browser Custom tracks Conservation tracks and inter-species navigation Hands-on session - Table Browser and Custom tracks

UCSC Archaeal Genome Browser

Table browser

UCSC Archaeal Genome Browser

Table browserTypically used for text based queries

For example:

Which tRNA genes in Pyrococcus furiosus have an overlap with an annotated protein coding region?

2 step query:

select all Refseq annotated coding regions

intersect this group with tRNA annotated regions

Typically used for text based queries

For example:

Which tRNA genes in Pyrococcus furiosus have an overlap with an annotated protein coding region?

2 step query:

select all Refseq annotated coding regions

intersect this group with tRNA annotated regions

Table browser 2set up query

Table browser 2set up query

Table browser 3Table browser 3

UCSC Archaeal Genome BrowserCustom tracks

UCSC Archaeal Genome BrowserCustom tracks

• Allows addition of your data within the browser

• Supports compressed or uncompressed files, using

• Tab separated data in GFF, GTF, BED or WIG formats

• BED files support disjoint data

• WIG files support continuous valued data

• Allows addition of your data within the browser

• Supports compressed or uncompressed files, using

• Tab separated data in GFF, GTF, BED or WIG formats

• BED files support disjoint data

• WIG files support continuous valued data

Custom tracksCustom tracks

Custom tracks - examplesCustom tracks - examples

Custom tracks - example 2WIGgle tracks

Custom tracks - example 2WIGgle tracks

Conservation trackConservation track

UCSC Genome BrowserUCSC Genome Browser

• Advanced features:

• Table Browser

• Custom tracks

• Conservation track and inter-species navigation

• Advanced features:

• Table Browser

• Custom tracks

• Conservation track and inter-species navigation