Web-based analysis and annotation tools
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Transcript of Web-based analysis and annotation tools
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Web-based analysis and annotation tools
The Crown Human Genome Center & The National Lab for Genomic Infrastructure
Supported by the Ministry of Science
WIS Genome &Bioinformtics
Nili Avidan
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WIS Genome & Bioinformtics
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Use blast 2 sequence from BLAST tool to compare the new sequence to the known cDNA in the database
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Use BLAST 2 sequence with blastX as program to detect AA change
AA sequence from database
Your new DNA sequence
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WIS Genome &Bioinformtics
Kcourse.gif
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GESTALT figure of an analyzed genomic intervalGESTALT figure of an analyzed genomic interval
Blastn results of this genomic sequenceBlastn results of this genomic sequence
KIAA0001H963
WIS Genome &Bioinformtics
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H963 KIAA0001 K1LGR P2Y12
GPCR genes cluster(-strand)
aTRALPUSH(+strand) b
5’3’
5’ 3’
P2Y12LGR
NCBI clones
AC011103
AC078816
AC024886
AC020636
centromere telomere
76.9153. 0560.4175.00
71.18
54.07 62.34 55.60
57.33
Proscan promoter prediction
KB
WIS Genome &Bioinformtics
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mRNA sequencesmRNA sequences• Full mRNA sequences: RefSeq
WIS Genome &Bioinformtics
• Expressed Sequence Tags (ESTs): dbEST
• EST clusters: UniGene
• Predicted genes
• EST assemblies: – TIGR Human Gene Index – The HIB database of annotated UniGene clusters (MIPS) – AllGenes based on DoTS assemblies (U Penn.) – STACK (SANBI)
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H89282H89282
WIS Genome & Bioinformtics
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WIS Genome &Bioinformtics
*
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H89282H89282
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MIPS assembly H11548S1 length: 1373Contain 21 members
TIGR assembly THC394205length: 1373Contain 12 members
*Predicted protein annotation
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Multiple proteins alignment tool
Copy/past your protein and it ortholog/homolog here
Your E-mail
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MULTICLUSTAL alignment of the five GPCRsMULTICLUSTAL alignment of the five GPCRs
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Copy/Past you protein in the box
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Found two known motif Histidine acid phosphatase at AA391-405 and a Zinc finger at AA1269-1292
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WIS Genome &Bioinformtics
Kidney, embryonic cell line
Normal prostate tissue
Brain
Brain, primary tumor
Kidney, embryonic cell line
Brain, normal, Post-mortem
Brain, medulloblastoma
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Thank You!