BIF401 Midterm Current Paper Spring 2023

Subjective part

Question

1. PAM and Blosum difference.

PAM means “Point Accepted Mutation” Point accepted mutations means the substitution of one amino acid in a sequence with another that protein function remain conserved. BLOSUM matrices can be used to align the protein sequences. BLOSUM matrices was first purposed in 1992 by Henikoff et al. BLOSUM matrices is also called the Block substitution matrix without any gap although it has mismatches in sequences.

2. Uniprot and swissprot.

Both UniProt and SwissProt are the online database for proteins. UniProt is public database which is being used to search the sequence of proteins. SwissProt is the manually annotated version of the UniProt Database.

3. Rooted and unrooted Phylogenetic tree

Phylogenetic specifies evolutionary relationship with the help of trees. Trees can be rooted or unrooted. Rooted trees can show temporal evolutionary direction. Rooted trees are computationally expensive. Rooted trees shows the most basal ancestor of the tree. Unrooted phylogenetic tree does not show an ancestral root. Unrooted trees represents the branching order but do not indicate the root or location of the last common ancestor. Unrooted trees shows the relatedness of organisms without indicating ancestry.

Applications of bioinformatics in the field of GENOMICS and PROTEOMICS GENOMICS:

• Bioinformatics can help in assembling DNA sequencing data.
• It can help in gene finding (markers).
• Gene assembly can be performed using bioinformatics tools (nucleotide alignments)
• It can help transcribe the gene data to RNA data
• Also, databases can be generated from such data.

PROTEOMICS :

• Bioinformatics can help us in decoding protein sequences.
• It can also help us in understanding protein structure.