PROMoter SCanningANalysis tool

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PROMoter SCanningANalysis tool

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... tool to analyse a set of putative promoter sequences and recognize known and ... Sequences from Sergei Denissov, Molecular Biology (NCMLS) ... – PowerPoint PPT presentation

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Title: PROMoter SCanningANalysis tool

1

PROMoter SCanning/ANalysis tool

2
Goal

Creating a tool to analyse a set of putative
promoter sequences and recognize known and
unknown promoters, with built-in scoring system

3
Sequences to be PromScAnned

Sequences from Sergei Denissov, Molecular Biology
(NCMLS)
Obtained from the cloning of chromatin (U2-OS
human cells) highly enriched through double
immunoprecipitation with anti-TBP antibodies

4
Main database BLAT

BLAT BLAST-Like Alignment Tool
Aligns the input sequence to the Human Genome
Connected to several databases, like
mRNAs - GenScan
ESTs - TwinScan
RepeatMasker - UniGene
RefSeq - CpG Islands

5
BLAT Human Genome Browser
6
BLAT method (1)

Align sequence with BLAT, get alignment info
Per BLAT hit, pick up additional info from
connected databases
mRNAs
ESTs
RepeatMasker
CpG Islands
RefSeq Genes

7
BLAT method (2)

Additional info is gathered for four different
positions
1kb to the left query itself
1kb to the right query itself
20kb to the left query itself
20kb to the right query itself
(1 kb and 20kb can be adjusted through interface)

(close promoters)
(distant promoters)
8
mRNAs

Genbank human mRNAs are aligned against the
genome using the BLAT program. When a single mRNA
aligns in multiple places, the alignment having
the highest base identity is found. Only
alignments that have a base identity level within
1 of the best are kept. Alignments must also
have at least 95 base identity to be kept.

9
ESTs

This track shows alignments between human
Expressed Sequence Tags (ESTs) in Genbank and the
genome.
Expressed sequence tags are single read
(typically approximately 500 base) sequences
which usually represent fragments of transcribed
genes. Aligning regions (usually exons) are shown
as black boxes connected by lines for gaps
(usually spliced out introns).

10
RepeatMasker

Created by Arian Smit's Repeat Masker program
which uses the RepBase library of repeats from
the Genetic Information Research Institute
RepBase is a database of repetitive DNA sequence
elements found in a variety of eukaryotic
organisms including mammals, fish, insects,
nematodes, and plants.
Different Repeats SINE, LINE, LTR, DNA, Simple,
Low Complexity, Satellite, tRNA, other

11
CpG Islands

CpG CG C immediately followed by G
Particularly common near transcription start
sites, and may be associated with promoter
regions
Normally, in vertebrates CG -gt C is methylated
-gt methylated C is deaminated -gt TG
CpGs are relatively rare, unless there is a
selective pressure to keep them, or
a region is not methylated for some reason,
perhaps having to do with the regulation of gene
expression.
CpG islands are regions where CpG's are present
at significantly higher levels than is typical
for the genome as a whole.

12
RefSeq Genes

The RefSeq Genes track shows known protein coding
genes taken from mRNA reference sequences
compiled at LocusLink.
Refseq mRNAs are aligned against the genome using
the BLAT program. When a single mRNA aligns in
multiple places only the best alignments are
kept. The alignments must also have at least 98
sequence identity to be kept.

13
Scoring Method (1)

For each BLAT hit the Score is
S (length(mRNA)/distance(mRNA))sw
S (length(EST)/distance(EST))sw
S (length(RMSK tRNA)/distance(RMSK tRNA))sw
S (length(RMSK LTR)/distance(RMSK LTR))sw
S (length(RMSK rest)/distance(RMSK rest))sw
S (length(CpG)/distance(CpG))sw
S (length(RefSeq Genes)/distance(RefSeq
Genes))sw
(sw scoring weight)

14
Scoring Method (2)

Scoring weight reflects reliability of the
analyzed data how much proof for being
promoter?
Adjustable through interface defaults
mRNAs 4
ESTs 3
RepeatMasker tRNA 3
RepeatMasker LTR 2
RepeatMasker rest 1
CpG Islands 2
RefSeq Genes 0

15
DBTSS (1)

Additional info from DBTSS DataBase of
Transcriptional Start Sites
Most cDNAs lack precies information of 5
termini.
Oligo-capping method -gt full-length cDNAs.
Of about 284,687 5' end sequences obtained,
155,304 have been corresponded to cDNA sequences
of known genes (8,996 genes) and are presented in
the DBTSS

16
DBTSS (2)

Mapped each sequence on the human draft genome
sequence to identify its transcriptional start
site
Overall Score BLAT Score DBTSS Score

17
PromScan Query Interface

http//www.cmbi.kun.nl/timhulse/promscan

18
Output (1) Header
Excel also plain text format (tab separated)
possible
19
Output (2) Sequence Report
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Output (3) Overall Report
Multiple hits are sorted from high score to low
score the higher the score, the higher the
possibility the input sequence is a promoter.
21
Suggestions please!

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