These is the second part of the lecture slides of the BITS bioinformatics training session on the UCSC Genome Browser. See http://www.bits.vib.be/index.php?option=com_content&view=article&id=17203990:orange-genome-browsers-ucsc-training&catid=81:training-pages&Itemid=190

1. UCSC
genome browsing
Paco Hulpiau
http://www.bits.vib.be

2. TABLE GET CURRENT
BROWSER DNA BROWSER
GRAPHIC IN PDF
TO GET
OTHER
CLICK DATA
LINE

3. TO GET
OTHER
CLICK
LINE 2 DATA

4. Databases & accession numbers
§
GenBank exchanges data daily with its two partners in the
International Nucleotide Sequence Database Collaboration (INSDC):
European Bioinformatics Institute (EBI, part of EMBL)
DNA Data Bank of Japan (DDBJ)
§
Characteristics of GenBank and RefSeq @ NCBI :
GenBank RefSeq
Curated, NCBI creates from existing
Not curated, author submits
data
Multiple records for same loci Single records for each molecule
No limit to species included Limited to model organisms

5. Databases & accession numbers
§
§
The Ensembl automatic gene annotation system (Curwen et al, 2004) :
The gene-building system enables fast automated annotation of
eukaryotic genomes. It annotates genes based on evidence derived
from known protein, cDNA, and EST sequences
incl. GenBank sequences shared by INSDC, UniProtKB and NCBI
RefSeq

6. Databases & accession numbers
§ Database Typical accession numbers
GenBank AAA37420
NM_123456 = mRNA
NP_123456 = proteins
RefSeq
XM_123456 = predicted mRNA
XP_123456 = predicted proteins
UniProtKB (Swiss-
P12345, Q1AAA9
Prot/TrEMBL)
ENSMUSG00000123456 for Genes
Ensembl ENSMUST00000123456 for Transcripts
ENSMUSP00000123456 for Proteins

7. TO GET
OTHER
CLICK
LINE 2 DATA

27. zoom in on
exon 1 +
upstream

36. Exercises (II)
1) Are there any diseases related to your gene of interest? (OMIM)
Which interactions partners are known? (Entrez Gene)
Any important SNPs changing the amino acid sequence?
Get the multiple sequence alignment (MSA, multiz46way)
showing the nucleotide sequences of human, mouse, chicken,
Xenopus and zebrafish genes (CDS fasta alignment, exons not
separate).
Save your results (e.g. exercises2_1.doc).

37. 3
GET
DNA
TO GET
OTHER
DATA

40. http://www.visibone.com/colorlab
/

50. Exercises (II)
2) Get the DNA sequence for your gene of interest
including 2000 base pairs upstream and
use the following extended case/color options:
» RefSeq and Ensembl genes in bold
» SNPs (132) underlined
» Regulatory information e.g. from Oreganno and miRNA sites
in different colors
» Save your results (e.g. exercises2_2a.doc).

51. Exercises (II)
2) Try to get the DNA sequence for your gene of interest
in chicken or zebrafish and
use the following extended case/color options:
» UCSC, RefSeq and Ensembl genes in bold
» Other RefSeq genes underlined
» Human proteins in a specific color
» Save your results (e.g. exercises2_2b.doc).

52. 4
TABLE
BROWSER
TO GET
OTHER
DATA

59. COPY (Ctrl+C)

65. = Accession Number (RefSeq) e.g. NM_001229
= Gene Name (Entrez) e.g. CASP1

71. Exercises (II)
3) Get a list of the RefSeq and Ensembl transcripts using the table
browser with the following selected fields:
» name, chromosome, exon count, name2
» Save the results (exercises2_3a.xls)
Also get the sequences and save as genename_transcripts.fasta
Search the mouse genome using the filter in the table browser
to get all family members of a protein family (research interest)
and save the results in a list (exercises2_3b.xls) containing name,
chromosome, cds start and end, exon count and name2

72. TO GET
OTHER
DATA

73. TO GET
OTHER
DATA

75. BLAT = Blast-Like Alignment Tool
Ø search for high similarity matches by indexing entire
genome
Ø DNA limit = 25000 bases, for multiple seqs 50000 bases
Ø protein limit = 10000 aa, for multiple seqs 25000 aa
Ø total sequences = 25

76. PASTE (Ctrl+V)

85. TTTAGCCAACGAACAGTCGCT TTCTCTTTGCATCTGTCCCAG

88. §
The Utilities page contains links to some tools
created by the UCSC Genome Bioinformatics Group.
§
DNA Duster & Protein Duster remove non-sequence
related characters from an input sequence.

91. Exercises (II)
4) Use BLAT to find orthologs of your gene in chicken, zebrafish
and fruit fly. What is the genomic location?
Are the flanking genes the same?
Perform an in silico PCR to see what happens when more than 1
PCR product may arise and determine product size and Tm:
species: human
forward primer: TTC AAG GAG GCC TTC TCC CT
reverse primer: CTG GGG GAG AAG CTG A (+click flip reverse)