UCSC Archaeal genome browser

UCSC Archaeal genome browser

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

http://archaea.ucsc.edu

UCSC Archaeal Genome Browser

http://archaea.ucsc.edu

UCSC Archaeal Genome Browser

sample search for “regulatory proteins”

UCSC Archaeal Genome Browser

sample search for “regulatory proteins”

coordinates and annotated direction,

using Genbank, Tigr and Rfam

conservation

predictedpromoters and

terminators

Short sequence searching

Short sequence searching

Short sequence inputShort sequence input

Sequence searching - BLAT

Sequence searching - BLAT

search with either nucleotide or protein sequence

BLAT resultsBLAT results

BLAT result - detailBLAT result - detail

BLAT result - browserBLAT result - browser

BLAT search - multiple hits

BLAT search - multiple hits

BLAT- multiple hit response

BLAT- multiple hit response

BLAT - tRNA D armBLAT - tRNA D arm

in-silico PCR primer search

in-silico PCR primer search

in-silico search results

in-silico search results

UCSC Genome BrowserPCR Results -

UCSC Genome BrowserPCR Results -

UCSC Genome Browserreview

UCSC Genome Browserreview

Searching Text annotation- name and description

Short sequence Blat - protein or nucleotide sequence

in-silico PCR

Searching Text annotation- name and description

Short sequence Blat - protein or nucleotide sequence

in-silico PCR