20.02.20 External databases/ Bioinformatic resources

Question 1

What are external bioinformatic databases

Answer 1

Databases that store biological data information

Question 2

Types of bioinformatic databases

Answer 2

• Genome/sequence
• Gene expression
• transcriptomics
• proteomics
• epigenetic

Question 3

What two types of DNA databases are there

Answer 3

• Primary: contain experimentally derived data

- Secondary: data produced from the analysis of primary data

Question 4

Examples of Primary DNA databases

Answer 4

• EMBL-EBI: European Molecular Biology Laboratory- European Bioinformatics Institute. Ensembl= genome browser, BLAST/BLAT= sequence search
• GenBank (NCBI- National Centre for Biotechnology Information). Contains DNA sequences from a group of sources (Genbank, refseq) for 300,000 organisms
• DNA databank of Japan= nucleotide sequence and evolution data.

Question 5

Examples of secondary DNA databases

Answer 5

• OMIM (Online Mendelian Inheritance in Man)= contains genotype-phenotype information on mendelian disorders.
• RefSeq= annotated references for genomic, transcriptomic and protein data.
• 1000 genome project= data is available on the Ensembl platform
• HapMap= Map of haplotype regions and SNPs within them.

Question 6

What is phastCons and phyloP scores

Answer 6

-Used for phylogenetic and evolutionary conservation predictions. Models are used in UCSC genome browser and other variant classification software (Alamut).

Question 7

What is Human splicing finder

Answer 7

a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence.

Question 8

What is gnomAD

Answer 8

• Genome aggregation database

- Large population dataset from unrelated individuals. 125,748 exomes, 15,708 genomes

Question 9

What is Alamut Visual

Answer 9

-Software that incorporates multiple datasets from different sources to allow user friendly and efficient variant classification and genome interrogation.

Question 10

Examples of gene expression databases

Answer 10

• ArrayExpress: archived functional genomic data from microarray and sequencing platforms.
• Human protein atlas: expression profiles of human protein coding genes expressed in mRNA and protein levels and in multiple tissue levels.

Question 11

Examples of transcriptomic databases

Answer 11

• miRBase (microRNA database) from Manchester Uni= published miRNA sequences and annotation.
• Rfam= Collection of RNA families, represented by multiple sequence alignments, consensus secondary structures.

Question 12

Examples of protein sequence databases

Answer 12

• Disprot: database of manually curated experimental disorder evidence.
• Interprot: provides functional analysis of proteins.
• Pfam (EMBL-EBI): collection of protein families shown as multiple sequence alignments and hidden Markov Models. Enables identification of protein domains
• Uniprot and Swissprot (EMBL-EBI): Curated protein sequence information
• NCBI (National centre for Biotechnology Information): database of nucleotides, genomes, SNPs, proteins.
• Protein databank: archive of macromolecular structure data (X-ray, NMR).

Question 13

Protein interaction databases

Answer 13

• BioGRID (Biological Gnereal Repository for interaction datasets): archive of protein interaction data from model organsisms and human studies.
• RBPDB: database of RNA-binding protein specificity.

Question 14

What is Cancer genome atlas (TCGA)

Answer 14

-Epigenomic, transcriptomic and proteomic data from 20,000 cancer patients and matched controls for 33 cancer types.

Question 15

What is MethBase

Answer 15

Reference methylomes from different organisms.