mcb7300 bioinformatics lab1 - ohio university...pam (point accepted mutation): for evolutionary...
TRANSCRIPT
![Page 1: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/1.jpg)
Bio-Informatics LecturesA Short Introduction
![Page 2: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/2.jpg)
The History of Bioinformatics
![Page 3: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/3.jpg)
Sanger Sequencing
PCR in presence of fluorescent, chain-terminating dideoxynucleotides
![Page 4: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/4.jpg)
Massively Parallel Sequencing
![Page 5: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/5.jpg)
Massively Parallel Sequencing
Illumina/Solexa
![Page 6: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/6.jpg)
Roche/454, Emulsion PCR
Metzker, Nature Review: Genetics (11):31-46
![Page 7: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/7.jpg)
Illumina/Solexa: Solid-Phase Amplification
![Page 8: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/8.jpg)
![Page 9: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/9.jpg)
![Page 10: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/10.jpg)
![Page 11: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/11.jpg)
![Page 12: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/12.jpg)
![Page 13: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/13.jpg)
![Page 14: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/14.jpg)
![Page 15: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/15.jpg)
![Page 16: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/16.jpg)
![Page 17: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/17.jpg)
![Page 18: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/18.jpg)
http://www.genome.gov/sequencingcosts/
![Page 19: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/19.jpg)
http://www.genome.gov/sequencingcosts/
![Page 20: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/20.jpg)
~200 million sequences
1000 billion basesGrowth of GenBank and WGS
http://www.ncbi.nlm.nih.gov/genbank/statistics
![Page 21: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/21.jpg)
Growth of UniProtKB/TrEMBL
http://www.ebi.ac.uk/uniprot/TrEMBLstats
![Page 22: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/22.jpg)
How Does the Sequence Information Tell Us?
![Page 23: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/23.jpg)
How Does the Sequence Information Tell Us?
Bio-Informatics
![Page 24: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/24.jpg)
Scope of this lab
DATABASES: GenBank-http://www.ncbi.nlm.nih.gov EMBL-http://www.ebi.ac.uk DDBJ-http://www.ddbj.nig.ac.jp
Sequence Search and Retrieval: BLAST Sequence Alignement: ClustalW2, MAFFT Sequences Analysis and Domain Search: Pfam and SMART Protein Structure and Prediction: Pymol Molecular Evolution: MEGA
1. Be familiar with sequence databases and some online bioinformatics tools
http://www.ebi.ac.uk/services/all
More Tools to Discover on Your Own
http://www.expasy.org
![Page 25: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/25.jpg)
Online Tools
![Page 26: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/26.jpg)
Scope of this lab
2. Touch Some Simple Programming (Stand-alone)
Basic UNIX Commands: cd, mkdir, mv. cp, rm, cat, ls, pwd, gunzip, unzip, tar
Perl: String, Array, Hash
R: Read a file, column, row, plot, hist, heat map
![Page 27: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/27.jpg)
Beginning with a DNA Sequence
![Page 28: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/28.jpg)
Proteins
The primary sequence, structure, and function
of a protein are inter-related
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG
N-termnus
C-termnus
![Page 29: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/29.jpg)
Database Sequence Similarity Searching
Definition: Applies computation, mathematical algorithms, statistical inference to rapidly find similar sequences (hits) to a target (query) sequence from a database.
All similarity searching methods rely on the concepts of alignment between sequences.
A similarity score is calculated from a distance: the number of DNA bases or amino acids that are different between two sequences.
![Page 30: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/30.jpg)
Edit Distance
![Page 31: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/31.jpg)
Edit Distance
![Page 32: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/32.jpg)
Sequence Alignement and Dynamic Programming
![Page 33: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/33.jpg)
Sequence Alignement Comparison and Substitution Matrix
Some popular scoring matrices are:
PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required.
BLOSUM (BLOcks amino acid Substitution Matrix): for finding common motifs. For example in BLOSUM62, the alignment is created using sequences sharing no more than 62% identity.
Experimentation has shown that the BLOSUM-62 matrix is among the best for detecting most weak protein similarities.
![Page 34: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/34.jpg)
Sequence Alignement Comparison and Substitution Matrix
Some popular scoring matrices are:
PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required.
BLOSUM (BLOcks amino acid Substitution Matrix): for finding common motifs. For example in BLOSUM62, the alignment is created using sequences sharing no more than 62% identity.
Experimentation has shown that the BLOSUM-62 matrix is among the best for detecting most weak protein similarities.
![Page 35: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/35.jpg)
Sequence Alignement Comparison and Substitution Matrix
Some popular scoring matrices are:
PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required.
BLOSUM (BLOcks amino acid Substitution Matrix): for finding common motifs. For example in BLOSUM62, the alignment is created using sequences sharing no more than 62% identity.
Experimentation has shown that the BLOSUM-62 matrix is among the best for detecting most weak protein similarities.
![Page 36: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/36.jpg)
Sequence Alignement Comparison and Substitution Matrix
Some popular scoring matrices are:
PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required.
BLOSUM (BLOcks amino acid Substitution Matrix): for finding common motifs. For example in BLOSUM62, the alignment is created using sequences sharing no more than 62% identity.
Experimentation has shown that the BLOSUM-62 matrix is among the best for detecting most weak protein similarities.
![Page 37: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/37.jpg)
Sequence Alignement Comparison and Substitution Matrix
![Page 38: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/38.jpg)
Sequence Alignement Comparison and Substitution Matrix
Log-odds matrices
![Page 39: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/39.jpg)
Local and Global Alignements
Smith-Waterman
Needleman-Wunsch
![Page 40: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/40.jpg)
BLAST/FASTA Search and k-Tuple Method
![Page 41: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/41.jpg)
Use proteins for database similarity searches when possible
![Page 42: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/42.jpg)
![Page 43: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/43.jpg)
Lab 1
Sequence Search and Retrieval: BLAST Sequence Alignement: ClustalW2, MAFFT Sequences Analysis and Domain Search: Pfam and SMART Protein Structure and Prediction: Pymol Molecular Evolution: MEGA
Sequence Format - Fasta
>AT4G05320 ATGCAGATCTTTGTTAAGACTCTCACCGGAAAGACAATCACCCTCGAGGTGGAAAGCTCCGACACCATCGACAACGTTAAGGCCAAGATCCAGGATAAGGAGGGCATTCCTCCGGATCAGCAGAGGCTTATTTTCGCCGGCAAGCAGCTAGAGGATGGCCGTACGTTGGCTGATTACAATATCCAGAAGGAATCCACCCTCCACTTGGTCCTCAGGCTCCGTGGTGGTATGCAGATTTTCGTTAAAACCCTAACGGGAAAGACGATTACTCTTGAGGTGGAGAGTTCTGACACCATCGACAACGTCAAGGCCAAGATCCAAGACAAAGAGGGTATTCCTCCGGACCAGCAGAGGCTGATCTTCGCCGGAAAGCAGTTGGAGGATGGCAGAACTCTTGCTGACTACAATATCCAGAAGGAGTCCACCCTTCATCTTGTTCTCAGGCTCCGTGGTGGTATGCAGATTTTCGTTAAGACGTTGACTGGGAAAACTATCACTTTGGAGGTGGAGAGTTCTGACACCATTGATAACGTGAAAGCCAAGATCCAAGACAAAGAGGGTATTCCTCCGGACCAGCAGAGATTGATCTTCGCCGGAAAACAACTTGAAGATGGCAGAACTTTGGCCGACTACAACATTCAGAAGGAGTCCACACTCCACTTGGTCTTGCGTCTGCGTGGAGGTATGCAGATCTTCGTGAAGACTCTCACCGGAAAGACCATCACTTTGGAGGTGGAGAGTTCTGACACCATTGATAACGTGAAAGCCAAGATCCAGGACAAAGAGGGTATCCCACCGGACCAGCAGAGATTGATCTTCGCCGGAAAGCAACTTGAAGATGGAAGAACTTTGGCTGACTACAACATTCAGAAGGAGTCCACACTTCACTTGGTCTTGCGTCTGCGTGGAGGTATGCAGATCTTCGTGAAGACTCTCACCGGAAAGACTATCACTTTGGAGGTAGAGAGCTCTGACACCATTGACAACGTGAAGGCCAAGATCCAGGATAAGGAAGGAATCCCTCCGGACCAGCAGAGGTTGATCTTTGCCGGAAAACAATTGGAGGATGGTCGTACTTTGGCGGATTACAACATCCAGAAGGAGTCGACCCTTCACTTGGTGTTGCGTCTGCGTGGAGGTATGCAGATCTTCGTCAAGACTTTGACCGGAAAGACCATCACCCTTGAAGTGGAAAGCTCCGACACCATTGACAACGTCAAGGCCAAGATCCAGGACAAGGAAGGTATTCCTCCGGACCAGCAGCGTCTCATCTTCGCTGGAAAGCAGCTTGAGGATGGACGTACTTTGGCCGACTACAACATCCAGAAGGAGTCTACTCTTCACTTGGTCCTGCGTCTTCGTGGTGGTTTCTAA
![Page 44: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/44.jpg)
Lab 1 - BLAST
![Page 45: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/45.jpg)
Lab 1 - BLAST
![Page 46: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/46.jpg)
Lab 1 - BLAST
![Page 47: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/47.jpg)
E value: is the expectation value or probability to find by chance hits similar to your sequence. The lower the E, the more significant the score.
Lab 1 - BLAST
![Page 48: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/48.jpg)
Lab 1 - BLAST
![Page 49: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/49.jpg)
Lab 1 - BLAST
![Page 50: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/50.jpg)
Lab 1 - BLAST
![Page 51: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/51.jpg)
Lab 1 - BLAST
![Page 52: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/52.jpg)
Lab 1 - BLAST
![Page 53: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/53.jpg)
Lab 1 - Domain Search
![Page 54: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/54.jpg)
Lab 1 - Domain Search
![Page 55: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/55.jpg)
Lab 1 - Domain Search
![Page 56: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/56.jpg)
Lab 1 - Structure Visualization
Pymol
![Page 58: mcb7300 Bioinformatics Lab1 - Ohio University...PAM (Point Accepted Mutation): for evolutionary studies. For example in PAM1, 1 accepted point mutation per 100 amino acids is required](https://reader034.vdocuments.net/reader034/viewer/2022050118/5f4f19901d87343238134341/html5/thumbnails/58.jpg)
Lab 1 - Phylogenetics
UPGMA (Unweighted Pair Group Method with Arithmetic Mean)
Maximum likelihood
Maximum parsimony
Neighbor joining
MrBayes: Bayesian Inference of Phylogeny