BLAST and other \"quick\" alignment programs create an index of all the words, o

Question

BLAST and other "quick" alignment programs create an index of all the words, or k-mers, of size k in the query and target sequences, and look up matches in that index. In this problem, you will need to align the 10bp query to the 15bp target by filling in the k-mer table. There is no scoring scheme here and you can assume that a mismatch or two is permissible. Target sequence: base #: 111111 123456789012345 CTACGGGATCATTGC Query sequence: base #: 1234567890 ATCGGAATCA. i. Carefully draw the following table in your answer book and fill in the k-mer word locations and frequencies. All relevant k-mers are shown and sorted in alphabetical order. ii. Write the target and query sequences in your answer book and underline the 3-mer matches in the sequences. iii. If you can connect any pairs of matches to extend a match, show the alignment and extension. iv. Write out the alignment for any matches that could be extended.

Explanation / Answer

1. k-mers

ii.

CTACGGGATCATTGC
I I I I I I I I I I I I I
ATCGGAATCA

iii.

CTACGGGATCATTGC
I I I I I I I I
AT CGGAATCA

iv.

CTACGGGATCATTGC
I I I I I I I I
AT CGGAATCA

Start location of word is WORD TARGET QUERY AAT AAT GAT ACG TCG ATC ATC ACG TCG ATT TCA ATC CAT ATC TCA CGG GGG TCG CTA ATC TCG GAA GGG GGA GAT AAT GAA GGA GGG GAA GGG GGA GAA TAC TCG ATC TCA TCA ATC TCA TCA ATC TCG ACG ATC TGC TCA ATC TTG ATC TCA

Related Questions

Navigate

• Browse (All)
• Browse B
• Subjects

---

---

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.