Sequence Alignment and Computational Genomics: Pairwise and Multiple Alignment (BLAST, FASTA, Clustal), Scoring Matrices

In multiple sequence alignment (MSA), the Sum of Pairs (SP) score sums the scores of all pairwise alignments in each column:

This calculation includes pairwise substitution scores (matches and mismatches) and pairwise gap costs/penalties between each pair of residues.
The isolated "number of gap penalties" is not counted as an independent score; rather, specific gap costs associated with pairwise residue-gap and gap-gap alignments are computed.

Pairwise alignment tools and servers:
BCM Search Launcher and SIM are specialized online tools/interfaces designed specifically for pairwise sequence alignment.
BLASTN directly aligns nucleotide sequence pairs (or database searches).
BLASTX compares a translated 6-frame nucleotide query against a protein database, making it a translated search tool rather than a standard pairwise sequence alignment resource for homologous direct pairs.
According to the official key, Option 1 (BLASTX) is the correct answer.

Primary objectives of sequence alignment and comparison in bioinformatics include:

• Identifying conserved motifs and shared functional patterns (Option 1).
• Inferring phylogenetic relationships and evolutionary ancestry (Option 3).
• Detecting evolutionary conservation across species (Option 4).
  
  Direct sequence comparison does not investigate the macroscopic physical characteristics (e.g., solubility, density, melting point) of molecules. Hence, Option 2 is not a purpose of sequence comparison.