NCBI New Database -- Protein Clusters

Protein Clusters is a collection of related protein sequences (clusters). These clusters consist of Reference Sequence (ie, RefSeq = comprehensive, integrated, non-redundant sets of sequences) proteins which are encoded by prokaryotic and chloroplastic plasmids and genomes.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=proteinclusters

NCBI Genes and Disease Page

This resource is aimed at consumer health needs, but its generic information about genetic diseases might be useful to the student researchers. It has splendid links to other NCBI resources such as OMIM.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=gnd.TOC&depth=2

An amusing NCBI taxonomy site has extinct critter's DNA:
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=extinct

Seminar - May 23 - noon-2:00

The Genomics Shared Service presents:
Empowering Genomic Discoveries with Agilent Microarray Platform

Agilent Technologies is at the forefront of integrated genomics, offering solutions for gene expression profiling, miRNA, chromosomal copy number detection (CGH), transcription factor binding (ChIP-chip), methylation, alternative splicing and informatics. Learn how advancements with Agilent’s inkjet printing flexibility and free online design tools can be leveraged to further enable the research community at the University of Arizona.

Speaker: Christopher Hopkins, Ph.D. Agilent Technologies
Location: Kiewit Auditorium, Arizona Cancer Center
Date: Wednesday, May 23, 2007
Time: Noon ­ 2 p.m., LUNCH WILL BE PROVIDED.

Come see what the latest addition to the Genomics Shared Service can do
for your research.

Seminar - May 24 at 8am

The College of Medicine invites you to attend the special seminar of Dr.
Lisa Rimsza, who will be visiting the University of Arizona as a candidate
for the Head of Pathology. Please join us for this exciting presentation!

COLLEGE OF MEDICINE SPECIAL SEMINAR
Thursday, May 24: 8:00 - 9:00am
College of Medicine, room 8403
Translational Research in Lymphoma: Using Gene Expression Profiling to
Find and Expose "Immunostealth"

NCBI: Microbial Genome Notes - morning

Hand-out
ftp://ftp.ncbi.nih.gov/pub/minicourses/CURRENT/HO/PDF/Microbial.pdf
Primary page
http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
NCBI -- http://www.ncbi.nlm.nih.gov/ -- Instructors
Susan Dombrowski / Wayne ....
Help
blast-help@ncbi.nlm
301-496-2475

Outline
Entrez / pubmed & MynNCBI / BLAST / spec resources
Use
Entrez >> subject / text
BLAST >> sequence / pcr reaction -- http://www.ncbi.nlm.nih.gov/BLAST/
Entrez
PubMed / taxonomy (lineage) / VAST / BLAST / Phylogeny
interlinked - related sequences btw db
neighboring - inside a db
30 db -- new Protein Clusters (UniGene for protein)
Groups -- nucleotides / pubmed / taxonomy / proteins
-- Search _ all[filter]_ = current content of db
Types of db
primary db (orig data, controlled by submitter)
derived db (blt from primary, controlled by ncbi)
Searching
Help manual in entrez books - http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpbook.TOC
All db / cross db -- http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
default = search everywhere
Tabs = limit (fields, preview index)
[orgn] = organism field
entry Number = code
XM = experimental
icon -
MyNCBI
SDIs / "google alerts"
BLAST - http://www.ncbi.nlm.nih.gov/BLAST/
"basic local alignment search tool"
- very basic BLAST! >> no scoring, no statistics
- local, isolated, surprising reguions of similarity
- breaks seq into words
- hits become "seed" for alignment extension
- search algorithms .. smith-waterman - "local alignment"
- global alignment - end to end for pockets of similarity
- local alignment - matches letter by letter, not sequence by sequence (?) .... http://en.wikipedia.org/wiki/Local_alignment
- word size in nuc = exact match
- word size in proteins -- flexible matching (exact or "neighbohood words" - amino acid residues that are similar / biochem equiv) -
NR = non redundant protein = default db
LIMITS - organism
To exclude = _all[filter] NOT mammals_
Algorithm parameters - higher Expect Value, lower stringency
short sequence strategy ....
long sequence strategy (eval high
Precomputed services
- nuc or prot = related sequences
- blast link = Blink (like related sequences)
- transcript clusters = UniGene
- protein homologs = Homologene
DBS
Nucleotide -- Links / Related == can Sort Related Sequences - chose how
Genbank - No protein sequences
Protein >> BLink = related prot seques
Genome >> book links, many seque pub as texts
-- shotgun: http://www.ncbi.nlm.nih.gov/Genbank/wgs.html
-- browse genome trees

Bits
GC=guanine-cytosine content (GC-content) is a characteristic of the genome of any given organism -- http://en.wikipedia.org/wiki/GC-content

Ideas
MyNCBI set up for Bio5 researchers
(Elvis lives .. short sequence stragey)

NCBI workshops on campus - May 2007

5/15
Entrez Search Engine and the BLAST : Microbial Genomes resources
5/23
Exploring 3D Molecular Structures Using NCBI Tools
5/24
NCBI PubChem Workshop

http://biotech.arl.arizona.edu/education/events/2007/ncbi_courses.php

Molecule of the Day

Molecule of the Day provides something to chat about with faculty and students. Many of the daily postings are amusing.

I enjoy Pharyngula, too, but it's much more opinionated.

COM seminar

The College of Medicine invites you to attend the special seminar of Dr.
Christopher Corless, who will be visiting the University of Arizona as a
candidate for the Head of Pathology. Please join us for this exciting
presentation!

COLLEGE OF MEDICINE SPECIAL SEMINAR
Friday, May 11, 8:00 - 9:00am
College of Medicine, room 2117

University of Arizona Bio5 Librarians

Events and ideas of interest to the group.