Pages From 5thwmc_workshop-2

Burkholderia Gene Search

Search by: Locus G Gene Symbol S b l Common Name All Annotation

Gene Page : NT01BPA0352

General Gene Page Organization ƒ Annotation Display à Functional Curation Datatypes - Putative identification, Gene symbol, EC # - GO terms and Cellular role category - Gene/protein length, coordinates, MW, pI - Comments and additional supporting pp g information - Genome Properties - Community C i curation i

ƒ Column Task Bar

Gene Page : NT01BPA0352

Gene Page : NT01BPA0352

Gene Page : Gene Ontology Display

The Gene Ontology: AmiGO

The Gene Th G Ontology O t l http://www.geneontology.org/

Gene Page : NT01BPA0352

Community Curation Tool

Community Curation Example

Notation for: Pending Approved

General Gene Page Organization ƒ Column Task Bar à Annotation - Annotation Display - Nucleotide and protein sequence - Pubmed search results - Gene Ontology

à Evidence à Analysis

Gene Page : Sequences

Gene Page : PubMed Search

General Gene Page Organization ƒ Column Task Bar à Annotation

à Evidence - Gene Graphic -

TIGRFAM & PFAM matches Identification Alignment TmHMM Information COG Display Membrane Protein Information

- Protein vs All Alignment - Region View / Compare Regions à Analysis a ys s

Gene Page : Gene Graphic

Gene Page : TIGRFAM & Pfam

Gene Page : Identification Alignment

Gene Page : TmHMM

The Center for Biological Sequence Analysis Technical University of Denmark http://www.cbs.dtu.dk/services/TMHMM/

Gene Page : COGs

Clusters of Orthologous Groups of proteins (COGs) NCBI http://www.ncbi.nlm.nih.gov/COG/

Gene Page : Membrane Protein

Currently not functional

All vs. Protein Alignment g ƒ All of the p proteins in Pathema are routinely y blasted

against one another and the blast results are stored in the database. ƒ When a new genome is added to the database the all

vs. allll searches h are re-run. ƒ The information from the All vs. s All blast searches is

displayed throughout Pathema for cross genome analyses. analyses

Gene Page : Protein vs All Alignment

Pairwise Alignment Example Summary statistics off all ll alignments li t Detailed statistics of each alignment

Query nucleotide sequence Query protein translation M t h protein Match t i alignment li t

Multiple Sequence Alignment E Example l

Gene Page : Region View

Gateway Page

Gene Page : Compare Regions

General Gene Page Organization ƒ Column Task Bar à Annotation A t ti à Evidence

à Analysis - Ge Gene e Codo Codon Count Cou t - GC Content Display - 3rd Postion GC Skew - Primer Search

Gene Page : Gene Codon Count

Gene Page : GC Content Display

Gene Page : 3rd Position GC Skew Purpose: Find the best potential Open Reading Frames (ORFs) in this sequence based b d on third hi d position ii GC Skew. This tool works only in GC rich organisms because position 1 & 2 are constrained t i d by b the th genetic ti code, so the 3rd position is the only one where the higher GC content can exist.

Frame 1

ATGATGAG TACTACTAC

Frame 5

Frame 2

ATGATGATG TACTACTAC

Frame 4

Frame 3

ATGATGATG TACTACTAC

Frame 6

Gene Page : 3rd Position GC Skew

Highlighted Gene Tools & Lists

Highlighted Gene Tools & Lists

Burkholderia Blast

Highlighted Gene Tools & Lists

ƒ Future capabilities p of TCHAR: à Integrate into the CMR à Public availability: exportable/downloadable & BLASTable

Pathogenicity

LLNL Virulence Database

Pathogenicity

Burkholderia Virulence Factors

Comparative Analysis

Functional Genomics

htt // f http://pfgrc.tigr.org/ ti /

Mobile Elements

Latest Publications

Favorite Tools

What is the future of Pathema? ƒ We ea are e relying ey go on you your feedback! eedbac à Genome sequence analysis à Data exchange à Custom data analysis à Custom C t ttooll development d l t ƒ Continued data curation à Burkholderia Epitopes à Burkholderia mallei virulence factors à Other specialized gene lists …

Transporter Comparisons across Burkholderia Species

Mutidrug g Efflux Transporter p Families ƒ ABC: the ATP-binding ATP binding cassette superfamily ƒ MFS: the major facilitator superfamily ƒ MOP: the multidrug/oligosaccharidyl-

lipid/polysaccharide flippase superfamily ƒ RND: the resistance/nodulation/cell division superfamily - SMR: the small multidrug resistance subfamily

Organis sms

Drug Efflux Transporters Burkholderia sp. 383 Burkholderia pseudomallei 305 Burkholderia pseudomallei K96243 Burkholderia cenocepacia AU 1054 Burkholderia thailandensis E264 Burkholderia pseudomallei S13 Burkholderia pseudomallei Pasteur Burkholderia pseudomallei 668 B kh ld i pseudomallei Burkholderia d ll i 406e 406 Burkholderia pseudomallei 1710b Burkholderia pseudomallei 1710a Burkholderia pseudomallei 1655 Burkholderia pseudomallei 1106b Burkholderia pseudomallei 1106a Burkholderia mallei PRL-20 Burkholderia mallei 2002721280 Burkholderia mallei JHU Burkholderia mallei FMH Burkholderia mallei 10399

ABC

Burkholderia mallei NCTC10247

MFS

Burkholderia mallei 10229

RND

Burkholderia mallei SAVP1

MOP DMT(SMR)

Burkholderia mallei ATCC 23344 0

50

100

150

200

250

T Transporter t Count C t

Questions? Comments? Sugges o s Suggestions? [email protected]