(i) BLAST for Analyzing Sequence Similarity: The Basic Local Alignment Search Tool (BLAST) is a bioinformatics tool used to identify regions of local similarity between sequences.
BLAST compares a given DNA or protein sequence against databases, utilizing matrices to score sequence alignments.
Alignment scores are calculated by rewarding matches and penalizing mismatches.
Top-scoring matches are ranked by their likelihood of being due to an ancestral relationship versus random chance. High similarity matches can identify genes or proteins of interest.
Confirmed matches are further analyzed using ENTREZ.
(ii) Computer Programs for Gene Prediction:
GeneMark predicts genes in bacterial genomes.
GENSCAN predicts genes in eukaryotic genomes.