Final answer:
Inputting more nucleotides into BLAST, like 1000 instead of 100, would result in more specific matches due to the reduction in coincidental matches. Differences between megablast and blastn can be explained by their word length settings, with megablast focusing on fewer but more specific matches. BLAST uses a scoring system to effectively find the best alignments in genomic databases.
Step-by-step explanation:
If you had more nucleotides to enter into BLAST, such as 1000 instead of 100, it would likely find more specific matches. The specificity of a nucleotide sequence match in BLAST typically increases with the length of the query sequence because there is a lower chance of finding a long sequence that matches purely by coincidence. Thus, a longer sequence provides more information for BLAST to find a precise match.
The difference in the number of matches output by megablast and blastn can often be attributed to the difference in word length used by these algorithms. Megablast uses a longer word length, resulting in fewer but more specific matches, whereas blastn, with a shorter word length, identifies more matches that may be less specific. This occurs because the longer word length requires a greater degree of similarity before the algorithm recognizes it as a match.
BLAST tackles the issues of the massive volume of data in GenBank and the potential for random similarities by segmenting sequences into short segments or words and comparing them simultaneously. This process, along with a scoring system that assigns points for matches and penalties for mismatches and gaps, allows BLAST to find alignments with high overall scores effectively.