Bioformatics Flashcards
What is Sequence analysis?
A comparison of genes within a species or between different species to show relations between species or protein functions. Determined genes that encode proteins and RNA genes.
Sangers sequence analysis
DNA Denaturation due to heat.
What is next-gen sequencing?
It generates masses of DNA sequence data that’s richer and more complete than sanger. Makes large scale whole genome sequencing possible for researchers.
Sequence Homology Software
BLAST. An algorithm which searches databases, to detect a specific query, then when it finds a match, it searches for shared nucleotides at the end of the seed to end the match.
Different types of BLAST?
BLASTN BLASTP PSI BLAST BLASTX MegaBLAST
BLASTN
Basic nucleotide sequence searches.
BLASTP
Used to search Amino Acid sequences.
PSI-BLAST
Analyses the relationships between divergently evolved proteins.
BLASTX & BLASTN variants
Six frame translation for protein and nucleotides respectively in the search.
MegaBLAST
BLASTs several sequences at once to cut down on processing and server reporting time.
Genome annotation
The marking of genes and other biological features in DNA sequencing.
Modelling evolutionary biology
Study of the origin and descents of species and there’s change over time.
Trace, compare, track.
GWAS
Examination of many common genetic variants in different individuals to see if they identify with a trait.
SNPs and traits of major diseases.
Gene expression analysis
Determines the gene implicated in a disorder. Comparison of cancerous and non cancerous cells to determine the transcripts (Up&Down Regulation).
Heatmaps
Show how a particular variable influenced gene expression.
Hierarchical clustering
Objects being more related to nearby objects than to those further away.
Analysis of protein expression
Protein microarrays
HT MS to provide a snapshot of the protein present in a biological sample.
Protein-Protein Interaction
Physical contact of two or more proteins as a result of a biological event or electrostatic forces. Enables creation of large protein interaction networks, empowers biochemical signalling and disease pathogenesis. Provides new therapeutic targets.
Network analysis
Understands the relationship with biological networks such as protein-protein interaction networks.
Network biology
Integrates many different data types which are connected either physically or functionally.
Three types of databases
Data from empirical methods i.e. gene knockout.
Predicted data.
Both.
Meta-database
Incorporates data compiled from multiple other databases.
Key databases
Nuclei can acid sequence databases.
Protein databases.
Meta-databases.
Nucleic acid sequence database
DNA sequence Genomics RNA sequence. GeneBank EMBL DDBJ.
