What are the differences among the following blast programs. What is used as the input (“query”) and what type of database is searched?
what are the gene ontology categories
molecular function
biological process
cellular compound
What is Gene Ontology?
A consortium that develops a common vocabulary to
describe the function of genes/proteins across taxa
what is ShinyGO
additional to GO output: graphical representation
what is PAML
analyze protein-coding gene sequences
to estimate the synonymous and nonsynonymous rates (dS and dN)
detect positive Darwinian selection driving protein evolution.
can do this by branch/ site specific search even if average is negative
what is Galaxy
Galaxy is a web-based platform for many types of genomic analyses
can be used to align coding sequences from protein alignments and calculate dN/dS
can run CODEML
CODEML is a program within the PAML
what is PAL2NAL
PAL2NAL converts a protein alignment into the corresponding codon-based DNA alignment.
which databases are searched using blastp?
UniProtKB/Swiss-Prot
(protein-protein)
Last changed7 days ago
