Summary
Samenvatting H3 "Bioinformatic and Functional Genomics"
- Course
- Institution
- Book
Samenvatting H3 "Bioinformatic and Functional Genomics", dit hoofdstuk gaat over pairwise alignments.
[Show more]
Connected book
Book Title:
Author(s):
- Edition:
- ISBN:
- Edition:
Seller
Follow
wendyvandermeulen
Reviews received
Content preview
Hoofdstuk 3: pairwise Alignments➢ Define homologs, paralogs, orthologs
♥ homology
♪ Similarity attributed to descent from a common ancestor.
♪ Orthologs
❖ Homologous sequences in different species that arose from a common ancestral gene during speciation; may
or may not be responsible for a similar function.
❖
• members of a gene (protein) family in various organisms.
♪ Paralogs
❖ Homologous sequences within a single species that arose by gene duplication.
❖
• members of a gene (protein) family within a species.
♪
➢ Perform pairwise alignments (NCBI BLAST)
♥ Pairwise sequence alignment is the most fundamental operation of bioinformatics
♪ It is used to decide if two proteins (or genes) are related structurally or functionally
♪ It is used to identify domains or motifs that are shared between proteins
♪ It is the basis of BLAST searching
♪ It is used in the analysis of genomes
, ♪
General approach to pairwise alignment
❖ Choose two sequences
❖ Select an algorithm that generates a score
❖ Allow gaps (insertions, deletions)
❖ Score reflects degree of similarity
❖ Alignments can be global or local
❖ Estimate probability that the alignment occurred by chance
♥ protein sequences can be more informative than DNA
♪ protein is more informative (20 vs 4 characters)
❖ many amino acids share related biophysical properties
♪ codons are degenerate: changes in the third position often do not alter the amino acid that is specified
♪ protein sequences offer a longer “look-back” time
♪ DNA sequences can be translated into protein, and then used in pairwise alignments
♪ Many times, DNA alignments are appropriate
❖ --to confirm the identity of a cDNA
❖ --to study noncoding regions of DNA
❖ --to study DNA polymorphisms
❖ example: Neanderthal vs modern human DNA
♥ Definition: pairwise alignment
♪ The process of lining up two sequences to achieve maximal levels of identity (and conservation, in the case of
amino acid sequences) for the purpose of assessing the degree of similarity and the possibility of homology.
♥ Definitions: identity, similarity, conservation
♪ Identity: The extent to which two (nucleotide or amino acid) sequences are invariant.
♪ Similarity: The extent to which nucleotide or protein sequences are related. It is based upon identity plus
conservation.
♪ Conservation: Changes at a specific position of an amino acid or (less commonly, DNA) sequence that preserve the
physico-chemical properties of the original residue.
➢ Understand how scores are assigned to aligned amino acids using Dayhoff’s PAM matrices
♥ Calculation of an alignment score
♪
♪ Doel: log odds
❖
♪ Dayhoff’s approach to assigning scores for any two aligned amino acid residues
The benefits of buying summaries with Stuvia:
Guaranteed quality through customer reviews
Stuvia customers have reviewed more than 700,000 summaries. This how you know that you are buying the best documents.
Quick and easy check-out
You can quickly pay through credit card or Stuvia-credit for the summaries. There is no membership needed.
Focus on what matters
Your fellow students write the study notes themselves, which is why the documents are always reliable and up-to-date. This ensures you quickly get to the core!
Frequently asked questions
What do I get when I buy this document?
You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.
Satisfaction guarantee: how does it work?
Our satisfaction guarantee ensures that you always find a study document that suits you well. You fill out a form, and our customer service team takes care of the rest.
Who am I buying these notes from?
Stuvia is a marketplace, so you are not buying this document from us, but from seller wendyvandermeulen. Stuvia facilitates payment to the seller.
Will I be stuck with a subscription?
No, you only buy these notes for $7.23. You're not tied to anything after your purchase.
Can Stuvia be trusted?
4.6 stars on Google & Trustpilot (+1000 reviews)
70089 documents were sold in the last 30 days
Founded in 2010, the go-to place to buy study notes for 15 years now
Recently viewed by you
Exam (elaborations) ·
PVL3703 EXAM ANSWERS PACK 2023 - PASS WITH DISTINCTION!
Summary ·
Jeugdzorg in beweging: Overzicht van alle collegestof
Summary ·
Samenvatting deeltoets 1 Familie en Gezin (70110181AY)
Summary ·
IGCSE History Revision - Germany Depth Study 1918-1945
Exam (elaborations) ·
3P’s EXAM Updated 2023 NSG6020 QUESTIONS AND ANSWERS.
Presentation ·
Presentación CONSTRUCCIONES-Construcción Sustentable
Exam (elaborations) ·
Bahama Bucks Recipe Test Question and answers rated A+ 2024
