Zkušenosti z Opendoor Workshop „Working with Human Genome Sequence“

Zkušenosti z Opendoor Workshop „ Working with Human Genome Sequence “ Hinxton, Cambridge, UK 23.-25. ledna 2006 MUDr. Marek Turnovec Ústav biologie a lékařské genetiky 2. LF UK a FN Motol 11. dubna 2006

Working with Human Genome Sequence ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Modul 1: Sequences Formats and Retrieval ,[object Object],[object Object],[object Object],[object Object]

Přístup k sekvencím ,[object Object],[object Object],[object Object],[object Object],[object Object]

Formát dat ,[object Object],[object Object],[object Object],[object Object]

Rozdíly ve formátech EMBL a GenBank/DDBJ ,[object Object],[object Object],[object Object],[object Object]

Zkratky použité ve formátu EMBL ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

EMBL 1/3 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

EMBL 2/3 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

EMBL 3/3 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

GenBank/DDBJ 1/3 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

GenBank/DDBJ 2/3 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

GenBank/DDBJ 3/3 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

FASTA >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX IENY >embl|AA961746|AA961746 or60c12.s1 NCI_CGAP_GC3 Homo sapiens cDNA clone IMAGE:1600246 3' similar to gb:M17885 60S ACIDIC RIBOSOMAL PROTEIN P0 (HUMAN);, mRNA sequence. ... actttttaaagaagtaagcctttatttccttgttttgcaaataaaactggctaagttggt tgctttttggtgattagtcaaagagaccaaatcccatatcctcgtccgactcctccgact cttccttggcttcaaccttagctggggctgcagcagcacgaggagcagctgtggtggcag cagcataggggcagcagcacaaaggcagatggatcagccaagaaggccttgaccttttca gcaagtgggaaggtgtaatccgtctccacagacaaggccaggactcgtttgtacccgttg atgatagaatggggtactgatgcaacagttgggtagccaatctgcagacagacactggca acattgcggacaccctccaggaagcgagaatgcagagtttcctctgtgatatcaagcact tcagggttgtagatgctgccattgtcgaacacctgctggatgaccagcccaaaggagaag ggggagatgttgagcatgttcagcagcgtggctttcgctggctccactttgtctccagtc ttgatcagctgcacatcactcaggatttcaatggtgcccttggagattttagtggtgata cctaaagctggaaaaaggaggtcttctcgggcccgagaccagtgttctgggctggcacag tgacttcacat popis sekvence

UniProt ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Komplexnější databáze ,[object Object],[object Object],[object Object],[object Object],[object Object]

Reference Sequence Project ,[object Object],[object Object],[object Object],[object Object],[object Object]

InterPro ,[object Object],[object Object],[object Object]

Expasy ,[object Object],[object Object],[object Object]

Module 2: de novo Analysis of Sequence ,[object Object],[object Object],[object Object]

Používané nástroje ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

B asic L ocal A lignment S earch T ool ,[object Object],[object Object],[object Object],[object Object]

B asic L ocal A lignment S earch T ool ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

PSI -BLAST ,[object Object],[object Object],[object Object],[object Object],[object Object]

http://www.ncbi.nlm.nih.gov/blast/

http://www.ncbi.nlm.nih.gov/gorf/

http://www.ncbi.nlm.nih.gov/spidey/ ,[object Object]

Module 3: Genome Browsing ,[object Object],[object Object]

Genome browsers – co nabízí? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Genome browsers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

+ dobrá provázanost s ostatními službami NCBI (PubMed)

+ přímočaré ovládání + dostupnost i starších sestavení

+ databáze genů potvrzených cDNA klony plné délky

+ různé pohledy + k dispozici i archiv (starší sestavení) + snadné získávání dat + „evidence“

VEGA – Ve rtebrate G enome A nnotated

BioMart ,[object Object],[object Object],[object Object],[object Object]

1 Co chceme prohledávát? (sestavení, organismus)

Module 4: Exploring Function and Disease ,[object Object],[object Object],[object Object],[object Object]

Exprese ve tkáních Podobné proteiny

Module 5: Sequence Variation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

SNP Ensembl -> Gene variation info

Další zdroje ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Module 6: Comparative Sequence Analysis ,[object Object],[object Object]

Homologní geny ,[object Object],[object Object],[object Object],[object Object],[object Object]

Nástroje ,[object Object],[object Object],[object Object],[object Object]

Zkušenosti z Opendoor Workshop „Working with Human Genome Sequence“

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Zkušenosti z Opendoor Workshop „Working with Human Genome Sequence“