Shared by 
Unlock all 17 pages
Get it free by sharing your own notes, buy just this one, or become a member and unlock documents with your plan.
How to unlock this document
Choose the way that suits you. Each one gives you all 17 pages to read online and the PDF to download.
Share your notes, unlock for free
2 free unlocks for every 5 approved uploads
- Upload your own lecture notes, assignments, essays or past papers
- PDF, Word, PowerPoint and Excel files all work, and you can send many at once
- We check each upload; you get a notification when it is approved
- Spend a free unlock on this document or any other, and keep it for good
- Shared under your public username, never your email
Then upload your notes from your profile.
Buy this document
$17 one-time payment
- All 17 pages of this document, yours to keep
- Download the PDF and read it any time, also offline
- No subscription and nothing to cancel
- Find it again any time under My Profile → Library
You log in or create a free account first, then pay securely.
Become a member
Unlock documents from the whole library, which keeps growing
- Choose any documents you like, up to your plan’s unlocks
- Documents you unlock stay yours, even if you cancel later
- Your unlocks start again with every renewal
- Secure checkout by Dodo Payments
You log in or create a free account first, then pay securely.
Compare the plansAlready a member, or bought this before? Log in to open it
About this document
- Pages
- 17 pages
- Price
- $17 one-time, yours to keep
- Membership
- Included in every plan
- Format
- Subject
- Bioinformatics, Biology
This document explains the concepts of homology, similarity, and identity in the context of pairwise alignment of protein sequences. It discusses how to assess the relatedness of proteins and the use of scoring matrices like PAM and BLOSUM. It is useful for understanding evolutionary biology and bioinformatics techniques.
What's inside
- Definition of homology, orthologs, and paralogs
- Assessing relatedness of proteins
- Pairwise alignment and the NCBI BLAST tool
- Conservative substitutions and percent similarity
- Scoring matrices: PAM and BLOSUM
Who it is for: Students studying bioinformatics, biology or related fields. (Undergraduate)
Share with classmates: WhatsApp Telegram X LinkedIn Facebook
Summary
Pairwise alignment is a method to compare two sequences, such as proteins. It helps to understand their evolutionary relationships and similarities. Students learn how to assess the degree of similarity and the possibility of homology between two molecules.
Homology, Similarity, Identity
Homologous sequences share a common evolutionary ancestry. Similarity and identity in sequences are assessed through pairwise alignment. Similar amino acids share similar biochemical properties.
Pairwise Alignment and Mutations
Pairwise alignment helps identify mutations that have caused divergence of sequences. Common mutations include substitutions, insertions, and deletions. These are referred to as gaps in the alignment.
Scoring Matrix
A scoring matrix is a quantitative system for pairwise alignments. The PAM matrix is based on accepted point mutations. The BLOSUM matrix is based on conserved positions in blocks of related sequences.
BLAST and Database Search
BLAST extends word pairs to find significant hits in a database. Database searches help find the function of a gene and related genes in other organisms. The E-value indicates the expected number of sequences that give the same score by chance.
Key terms
- Homologous sequences
- Sequences that share a common evolutionary ancestry.
- Orthologs
- Homologous sequences in different species that arose from a common ancestral gene.
- Paralogs
- Homologous sequences that arose by a mechanism such as gene duplication.
- Conservative substitutions
- Aligned residues that are similar but not identical because they share similar biochemical properties.
- PAM matrix
- A scoring matrix based on accepted point mutations in related protein sequences.
- BLOSUM matrix
- A scoring matrix based on conserved positions in blocks of related sequences.
Questions this document helps with
- What is the difference between orthologs and paralogs?
- How does pairwise alignment help in identifying mutations?
- What does the E-value in a database search signify?
Summary written with AI from the document's text.
Ask the AI Teacher
Ask any question about this document or your course, and get a clear explanation.
Log in to ask Create a free account
Free accounts can ask 5 questions a day.