Bioinformatics overview

Transcription

1 Bioinformatics overview Aplicações biomédicas em plataformas computacionais de alto desempenho Aplicaciones biomédicas sobre plataformas gráficas de altas prestaciones Biomedical applications in High performance computing platforms Oswaldo Trelles, PhD University of Malaga In this section we survery the bioinformatics application domain and the typical sources of data in the field

2 Definition Computer sciences, statistics, physics, chemistry,... Information Technologies Bioinformatics: The application of computational techniques to the management and analysis of biological data Molecular, clinic, population, environmental,... Acquisition, storage, retrieval, transmission, processing...

3 The domain of the data

4 Data production Huge data production at different levels Atoms Proteins Interactions Metabolic pathways Cells Organs Organisms Populations

5 Diversity of types of data > E bp DNA linear gaattctaac ggtcccgaaa ctctgtgcgg tgctgaactg gttgacgctc tgcagtttgt ttgcggtgac cgtggttttt attttaacaa acccactggt tatggttctt cttctcgtcg tgctccccag actggtattg ttgacgaatg ctgctttcgt tcttgcgacc tgcgtcgtct ggaaatgtat tgcgctcccc tgaaacccgc taaatctgct tagaagctt

6 Format heterogeneity LOCUS E bp DNA linear PAT 04-NOV-2005 DEFINITION DNA encoding human insulin-like growth factor I(IGF-I). ID E01306; SV 1; linear; unassigned DNA; PAT; SYN; 229 BP. ACCESSION E01306 AC E01306; VERSION E GI: DT 07-OCT-1997 (Rel. 52, Created) KEYWORDS JP A/1. DT 09-NOV-2005 (Rel. 85, Last updated, Version 3) SOURCE synthetic construct DE DNA encoding human insulin-like growth factor I(IGF-I). ORGANISM synthetic construct KW JP A/1. other sequences; artificial sequences. OS synthetic construct REFERENCE 1 (bases 1 to 229) OC other sequences; artificial sequences. AUTHORS Raasu,A., Toomasu,M., Berun,N. and Majiasu,U. RA Raasu A., Toomasu M., Berun N., Majiasu U.; TITLE METHOD FOR TRANSPORTING GENE PRODUCT TO MEDIUM PROPAGATING GRAM RT "METHOD FOR TRANSPORTING GENE PRODUCT TO MEDIUM PROPAGATING NEGATIVE BACTERIA GRAM JOURNAL Patent: JP A 1 20-AUG-1987; RT NEGATIVE BACTERIA"; KABIGEN AB RL Patent number JP A/1, 20-AUG COMMENT OS Artificial gene RL KABIGEN AB. OC Artificial sequence; Genes. CC OS Artificial gene OS Homo sapiens CC OC Artificial sequence; Genes. PN JP A/1 CC OS Homo sapiens PD 20-AUG-1987 CC CC strandedness: Single; CC strandedness: Single; CC CC topology: Linear; CC topology: Linear; CC CC hypothetical: No; CC hypothetical: No; CC CC anti-sense: No; CC anti-sense: No; CC FH Key Location/Qualifiers FH Key Location/Qualifiers CC FT mat_peptide FT /product='human insuline-like growth factor I CC FT CDS > FT CDS > CC FT /product="human insulin-like growth factor I" FEATURES Location/Qualifiers FH Key Location/Qualifiers source FT source /organism="synthetic construct" FT /organism="synthetic construct" /mol_type="unassigned DNA" FT /mol_type="unassigned DNA" /db_xref="taxon:32630" FT /db_xref="taxon:32630" ORIGIN SQ Sequence 229 BP; 40 A; 57 C; 55 G; 77 T; 0 other; 1 gaattctaac ggtcccgaaa ctctgtgcgg tgctgaactg gttgacgctc tgcagtttgt gaattctaac ggtcccgaaa ctctgtgcgg tgctgaactg gttgacgctc tgcagtttgt ttgcggtgac cgtggttttt attttaacaa acccactggt tatggttctt cttctcgtcg ttgcggtgac cgtggttttt attttaacaa acccactggt tatggttctt cttctcgtcg tgctccccag actggtattg ttgacgaatg ctgctttcgt tcttgcgacc tgcgtcgtct tgctccccag actggtattg ttgacgaatg ctgctttcgt tcttgcgacc tgcgtcgtct ggaaatgtat tgcgctcccc tgaaacccgc taaatctgct tagaagctt ggaaatgtat tgcgctcccc tgaaacccgc taaatctgct tagaagctt 229 // // The DNA encoding human insulin-like growth factor I(IGF-I) available at GenBank: E (search for insulin in All databases ) The same insulin (E01306) sequence at (in both text-boxes some lines has been removed)

7 Dispersion of data sources More than 1000 biological data collections Bioinformatics workflows: the usual way to work See: [1] Infobiogen: Catalog of Databases: Bioinformatics: a web-based domain

8 Types of data and applications (overview)

9 Sequencing data The long DNA chain is split in small fragments that are read using sequencing technology. Read: short sequences obtained during the sequencing process Software is used to obtain Contigs, Scaffolds, Consensus Reading in annotation data from a GFF file. Assigning aligned reads to exons and genes. Biologically intelligent interpretation of genomic data FASTA and FASTQ formats >000014_1863_0292 length=76 uaccno=fgsmdpn08etuie AATACTCAGGAATCGAACGGACTCGGGTATAGTATATGATCGGCAGCCAGCCG AACATAACAGCGGCATGAAAACC >000016_1821_0619 length=120 uaccno=fgsmdpn08ep50t GGCAAGTTTTCGGTGTCGCTAAGCCCGAGATATCGCAGCTCACCCGTGTCGGC GATTGCTGCTGTGACCGTCCCCAGTCGGTCACCCTCCGGCTGATTCTATCCTTACATCGG TCGTTTC >000021_1845_1786 length=69 uaccno=fgsmdpn08esarw ATCCGCGCGGCCGCATTGTCGACACTGCCTGCCGGCAGTGAAGGCGAGGCGCA GGTGGCCGATGCGCTG >000030_1849_0863 length=69 uaccno=fgsmdpn08esmpd ATCCGCGCGGCCGCATTGTCGACACTGCCTGCCGGCAGTGAAGGCGAGGCGCA GGTGGCCGATGCGCTG >000035_1856_0283 length=148 uaccno=fgsmdpn08es8dp GACGCCCTTTATGCACGTTTCGCTCACAGTATCCCTTAATAGCAAGATTAATA CCCTCAGTGGCCCCACTAGTAAAAACGATCTCTCGAGAACGACAGTTCAGTTC ATTGGCAATCAATTTTCGGGCCGTTTCTTACCGCCTCCTCAG

10 Assembling the puzzle From spectrograms to a sequence of letters An exhaustive and resource consuming procedure is needed to solve the assembling fragments into a longer Contigs... the sequence is coming up

11 Biological sequence data biológicas >ref NT_ : Drosophila melanogaster chromosome 2L CGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGG GAGAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAA TGGTGGCGGATGAACGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTT AAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCG TTCTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGAGAGAGAGCAGCGGAGATATT TAGATTGCCTATTAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTCTATATAATGAC TGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAATCGACAATGCACGACAGAGGAAGCAGAACAGAT ATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCGAGAGTAGTGC CAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATGGTGGCGGATGAACGAGATGATAATATATTC AAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGA GAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAA GACAATACACGACAGAGAGAGAGAGCAGCGGAGATATTTAGATTGCCTATTAAATATGATCGCGTATGCG AGAGTAGTGCCAACATATTGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAAC CCAAATCGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATAT TATAGGGAGAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTTGGCAAC CCAAAATGGTGGCGGATGAACGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGC AACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGC CTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGAGAGAGAGCAGCGGA GATATTTAGATTGCCTATTAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTCTATAT AATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAATCGACAATGCACGACAGAGGAAGCAGA ACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCGAGAG TAGTGCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATGGTGGCGGATGAACGAGATGATAAT ATATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGT ATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACC CAAAAAGACAATACACGACAGAGAGAGAGAGCAGCGGAGATATTTAGATTGCCTATTAAATATGATCGCG TATGCGAGAGTAGTGCCAACATATTGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACC GCAAACCCAAATCGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTC CCATATTATAGGGAGAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTT GGCAACCCAAAATGGTGGCGGATGAACGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATT CATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAAT GAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGAGAGAGAGC AGCGGAGATATTTAGATTGCCTATTAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCT CTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAATCGACAATGCACGACAGAGGA AGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATG CGAGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATGGTGGCGGATGAACGAGAT GATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGA TCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCG CAAACCCAAAAAGACAATACACGACAGAGAGAGAGAGCAGCGGAGATATTTAGATTGCCTATTAAATATG ATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTAT TTTACCGCAAACCCAAATCGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTT TCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTTTGA TTTTTTGGCAACCCAAAATGGTGGCGGATGAACGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAA TAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGT GCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGAGA GAGAGCAGCGGAGATATTTAGATTGCCTATTAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTG TGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAATCGACAATGCACGAC AGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCG From assembly to databases entries FASTA is the favorite format used for this type of data (without annotations) We knows the text, but the meaning needs more processing

12 Annotated Sequence databases ID 100K_RAT STANDARD; PRT; 889 AA. AC Q62671; DT 01-NOV-1997 (Rel. 35, Created) DT 01-NOV-1997 (Rel. 35, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE 100 KD PROTEIN (EC ). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. RN [1] RP SEQUENCE FROM N.A. RC STRAIN=WISTAR; TISSUE=TESTIS; RX MEDLINE; RA MUELLER D., REHBEIN M., BAUMEISTER H., RICHTER D.; RT "Molecular characterization of a novel rat protein structurally RT related to poly(a) binding proteins and the 70K protein of the U1 RT small nuclear ribonucleoprotein particle (snrnp)."; RL Nucleic Acids Res. 20: (1992). RN [2] RP ERRATUM. RA MUELLER D., REHBEIN M., BAUMEISTER H., RICHTER D.; RL Nucleic Acids Res. 20: (1992). CC -!- FUNCTION: E3 UBIQUITIN-PROTEIN LIGASE WHICH ACCEPTS UBIQUITIN FROM CC AN E2 UBIQUITIN-CONJUGATING ENZYME IN THE FORM OF A THIOESTER AND CC THEN DIRECTLY TRANSFERS THE UBIQUITIN TO TARGETED SUBSTRATES (BY CC SIMILARITY). THIS PROTEIN MAY BE INVOLVED IN MATURATION AND/OR CC POST-TRANSCRIPTIONAL REGULATION OF MRNA. CC CC This SWISS-PROT entry is copyright. It is produced through... CC DR EMBL; X64411; CAA ; -. DR PFAM; PF00632; HECT; 1. DR PFAM; PF00658; PABP; 1. KW Ubiquitin conjugation; Ligase. FT DOMAIN ASP/GLU-RICH (ACIDIC). FT DOMAIN PRO-RICH. FT DOMAIN ASP/GLU-RICH (ACIDIC). FT BINDING UBIQUITIN (BY SIMILARITY). SQ SEQUENCE 889 AA; MW; DD7E6C7A CRC32; MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN HPFFRRSDSM VYEYVRKYAE HRMLVVAEQP LHAMRKGLLD VLPKNSLEDL TAEDFRLLVN GCGEVNVQML ISFTSFNDES GENAEKLLQF KRWFWSIVER MSMTERQDLV YFWTSSPSLP ASEEGFQPMP SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV //