astrobiomike / bvcn-binder-prokka-htseq

Lesson and tutorial on annotating genomes and metagenomes with prokka, and associating read-mapping data with those annotations

Binder for BVCN Comparative Genomics lesson

Initially forked from here. Thank you to the awesome binder team!

Part of the Bioinformatics Virtual Coordination Network :)

Walkthrough (interspecies example with two homologous sequences)

Enter the first direcotry

cd interspecies_example//

Align the FASTA amino acid file

muscle -in MNBX01000583.1_4.faa -out MNBX01000583.1_4.fa

Make a codon alignment from the peptide alignment and nucleotide sequence

pal2nal.pl MNBX01000583.1_4.fa MNBX01000583.1_4.ffn -output fasta > MNBX01000583.1_4.codonalign.fa

Check that the correct input/output files are in the codeml.ctl file

less codeml.ctl

Run codeml

codeml codeml.ctl

Walkthrough (intraspecies example with three gene paralogs from one genome)

Enter the second directory

cd intraspecies_example/

Align the FASTA amino acid file

muscle -in NC_009928.1_232.faa -out NC_009928.1_232.fa

Make a codon alignment from the peptide alignment and nucleotide sequence

pal2nal.pl NC_009928.1_232.fa NC_009928.1_232.ffn -output fasta > NC_009928.1_232.codonalign.fa

Run codeml after checking out the input/output codeml.ctl file

codeml codeml.ctl

Walkthrough (PseudoHunter)

Print the PseudoHunter help menu

PseudoHunter.py -h

Run program on the test dataset

cd PseudoHunter/
cd mycobacterium/
PseudoHunter4.py -q Mycobacterium_leprae-subset.fna -r Mycobacterium_tuberculosis_H37Rv.fna -ctl ../codeml-2.ctl -out pseudohunter_out

Walkthrough (ParaHunter)

Print the ParaHunter help menu

Parahunter.sh -h

Run program on the test dataset

cd ParaHunter/
cd cyanothece/
ParaHunter.sh -a CyanothecePCC7425.faa -n CyanothecePCC7425.ffn -l ../codeml-2.ctl