lect 13 MSA

lect 13 MSA - Bioc 2808 Lecture 13 Multiple Alignments...

Info iconThis preview shows pages 1–8. Sign up to view the full content.

View Full Document Right Arrow Icon
Click to edit Master subtitle style 7/29/10 Bioc 2808 Lecture 13 Multiple Alignments Instructor Dr. Junwen Wang
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
7/29/10 Multiple Alignments Consistent alignments of more than two sequences. They allow us to examine families of (genes) proteins. We can: Understand our genes or proteins better Get more correct alignments Determine the extent of variability possible Identify functional or characteristic
Background image of page 2
7/29/10 Consistency Knowing how to align X to Y may be helped by knowing how Z will align to both. Standard progressive alignment will not look beyond X and Y. Consistency approaches try to reconcile the alignment of X and Y in terms of the alignment of them to all the “Z” sequences.
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
7/29/10 Alignment Policy Use proteins if possible – turn back to DNA later if you want Dealing with divergence: If sequences are too dissimilar, errors are very likely. Programs can be easily confused by chance, similarities scoring about the same as the distantly, but truly, related regions.
Background image of page 4
7/29/10 Alignment Policy Long insertions/deletions are difficult for programs How can the large gap penalty for the indel be accommodated? Semi-global and global methods may give very different results. Duplications, inversions, rearrangements cause similar problems:
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
7/29/10 Multiple Alignment Styles (a) Global alignment with gap insertion (b) Local alignment – find common local elements, regardless of order in sequence. Motif finding not globally aligning.
Background image of page 6
Types of Multiple Alignments There are many options. Some can give optimal solutions, most use “heuristics” to increase speed but may not be optimal. Exact methods – Dynamic
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 8
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 07/29/2010 for the course BIOC BIOC2808 taught by Professor Dr.jjwang during the Fall '09 term at HKU.

Page1 / 46

lect 13 MSA - Bioc 2808 Lecture 13 Multiple Alignments...

This preview shows document pages 1 - 8. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online