BIOS 390 Introduction to Bioinformatics

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BIOS 390 Introduction to Bioinformatics

• Instruments used in informatics

–Answer

• software (statistics, APIs, visualisation)
• algorithms (modelling, encryption -->analysis)
• Data driven science

–Answer start analysing, then formulate hypotheses

• Hypotheses driven science

–Answer formulate hypotheses, then generate data -->Bioinformatics at interface of data driven / hyp. driven

• 3 main categories of biological data

–Answer 1) sequence data 2) structural data (DNA, RNA, tissues) 3) functional data (interactions, ...)

• primary databases

–Answer hold original, raw data

• derived databases

–Answer specialized, agglomerated and curated databases from pri- mary databases (Uniprot, KEGG, Progene)

7. BAM 1 / 4

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–Answer compressed binary version of Sequence Alignment (SAM) --> reduced storage but not humanly readable. Way to store sequence information

• BED file format

–Answer way to store genomic sequence information (with extra info; not binary)

9. VCF

–Answer way to store sequence information.variant call format –Answer for genomic variation data-->logic compression. Give frequency

• logic compressino (e.g

–Answer VCF) –Answer only write down sequences that vary from a reference)

• Ontologies

–Answer objects, their hierarchies and relationships --> how to display / store ?

• hierarchical coding (CURIEs)

–Answer give tags; identify hierarchy of information by CURIEs

• APIs

–Answer Application Programming interfaces-->make data trasnferable from one software to another

• Use of APIs

–Answer -web API 2 / 4

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–Answer machine readable response to queries over HTTP -bioinformatics apps –Answer use APIs for data retrieval and display

• Meta-studies of Metadata

–Answer require APIs, softwares, ...-->retrieve metadata from different sources

• Bioinformatics vs computational biology

–Answer Bioinformatics –Answer use of computa- tional tools to make life sciences data more understandable CompBio –Answer development of mathematical and computational approaches to address theoretical and experimental questions in bio

• DNA (informationsgehalt)

–Answer genes –Answer stable, long-term storage

• RNA information

–Answer proteins –Answer amplification of specific parts, program execution

• Protein information

–Answer structure / function –Answer 3 / 4

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program execution

• interconversion of DNA to RNA (computational transcription)

–Answer straightfor- ward-->one RNA base for each DNA base

• interconversion of RNA to Protein

–Answer ambiguous –Answer multiple base triplets for same amino acids; six possible reading frames

• Homology

–Answer Descent from / similarity due to common ancestry

• Orthology

–Answer homology that derived during speciation --> still same function of genes

• Paralogy

–Answer parallel evolution after gene duplication (same ancestry) -->different functions possible

• Analogy

–Answer similarity without homology

• Sequence similarity

–Answer number of identical or related characters -->hard to find best batch –Answer also consider similarity of bases or only equality?

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