BCEM3201 - Protein Bioinformatics

Genomics

Study of complete genome

Transcriptomics

Analysis of all RNA transcripts (transcriptomes), reflecting gene expression

Proteomics

Investigation of all proteins (proteome) including structure and function

Metablomics

Study of small-molecule metabolites (metabolome) involved in cellular processes

ExPASy translate

Expert Protein Analysis System

Used to translate DNA or RNA sequence to protein sequence

ExPASy ProtParam

Computes various physical and chemical parameters for given protein

Half-life

Time it takes for half of protein amount in cell to disappear after its synthesis

Instability index

Protein with index less than 40 is stable, equal to or above 40 is unstable

GRAVY

Grand average of hydropathicity; sum of hydropathy values of all AAs divided by number of residues

Clustal Omega

Allows for comparison of sequences;

What does the * asterisk mean in Clustal Omega?

Positions which have single, fully conserved residue

What does the : colon mean in Clustal Omega?

conservation between groups of strongly similar properties

What does the . period mean in Clustal Omega?

conservation between groups of weakly similar properties

BLAST

Basic local alignment search tool

Compares protein or nucleic acid input with those in specific databases

BLAST searches for..?

regions of similarity, rather than aligning entire length of sequences

Max Score in BLASR

highest alignment score calculated from sum of rewards for matched nucleotides/AAs and penalties for mismatches and gaps

Total score in BLAST

sum of alignment scores of all segments from same subject sequence

Query coverage in BLAST

percent of query length included in aligned segments

Percent identity

highest percent identity for set of aligned segments to the same subject sequence

Expect (E) value

Number of alignments expected by chance.

Describes random background noise, and should be close to zero for significant alignments