NCBI Genome Browsers

Problem 1

• Genome Browser problem 1
• e.g. SNP in conserved region of genome across species. "Batch mode"

• USCS table browser - bulk
• assembly = genome sequence with new SNP
• start with "click here to reset"

1. Configure tracks and display
   • see the info that the genome browser can provide
2. Hide all tracks and submit
3. type gene name in field

• refseq - One entry per molecule/gene/mrna/protein. NCBI gen bank, people submit to genbank. A redundant database, find 10 different entries.
• changing display mode of an individual annotation track: hide, dense, **pack, squish
• Thick bar - exon
• forward or reverse strand, need to know where the promoter will be, so that's indicated by arrows on horizontal line
• important to add tracks from multiple sources in case genes annotated missed
• HGNC = Human Gene notation committee
• EST - expressed sequence tags
• click on laft side of genome browser, get
• "description page"
  • "Sequence and Links"
  • Click on Genomic sequence"
• what if want to know SNPs?
  • go to Variation
  • Some have indels as well.
• synonymous changes = NT change but AA no change
  • wobble - multiple code code forthe same AA
  • missence

Show me SNPS in conserved region

• Comparitive genomics section

Tsble browser, group= variation, then intersect with comparitive genomice, conversation

• rs prefix = reference SNP
  • BED output two columns is 0-based and 1-based
• NC chromosome, NG gene, NM mrna, NP protein
• zoom in by drag over region in genome browser

NCBI MAPVIEWER

• NCBI map = UCSC track
• reference assembly, from human genome sequencing project
• Add maps & objects to same region

ensembl

• ENSG - ensembl gene id
• more info adds more tabs across top
• variant effect predictor
• show transcript table
• SNP Annotation R = purine to purine, etc

ENSEMBL BioMart

• goal: 1000 nucleotide upstream sequence

1. Choose database
2. Choose dataset
3. Filters->gene>inpout external references id list> HGNC > "OTC"
4. Flanking to the gene or flanking to the transcript, if alternative splicing
5. header informatoin> uncheck ensembl gene id, associated gene name