Generated reciprocal best BLAST hits using Python script.

Test data generated locally using FASTA protein files made with Artemis,
and the underlying Python script for my Galaxy BLAST RBH tool available
from https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh

$ blast_rbh/blast_rbh.py NC_004547.faa chrA_prodigal.fasta -o rbbh_ref_vs_chrA_prodigal.tab -t blastp -a prot
Done, 3047 RBH found
Warning: Sequencies with tied best hits found, you may have duplicates/clusters

$ blast_rbh.py NC_004547.faa chrB_prodigal.fasta -o rbbh_ref_vs_chrB_prodigal.tab -t blastp -a prot
Done, 2839 RBH found
Warning: Sequencies with tied best hits found, you may have duplicates/clusters

$ blast_rbh.py NC_004547.faa chrC_prodigal.fasta -o rbbh_ref_vs_chrC_prodigal.tab -t blastp -a prot
Done, 3068 RBH found
Warning: Sequencies with tied best hits found, you may have duplicates/clusters

$ blast_rbh.py NC_004547.faa chrD_prodigal.fasta -o rbbh_ref_vs_chrD_prodigal.tab -t blastp -a prot
Done, 3066 RBH found
Warning: Sequencies with tied best hits found, you may have duplicates/clusters
Candidate orthologues, all RBBH to YP_052458 endo-1,4-D-glucanase

Picked from the set of RBBH from the four example strains
for having a moderate percentage identity:

$ grep YP_052458 rbbh_ref_vs_chr*.tab
rbbh_ref_vs_chrA_prodigal.tab:gi|50123291|ref|YP_052458.1|	1_3974	371	332	65	72	247	31.98	109
rbbh_ref_vs_chrB_prodigal.tab:gi|50123291|ref|YP_052458.1|	1_3948	371	332	65	72	248	35.08	114
rbbh_ref_vs_chrC_prodigal.tab:gi|50123291|ref|YP_052458.1|	1_114	371	332	65	71	247	32.79	104
rbbh_ref_vs_chrD_prodigal.tab:gi|50123291|ref|YP_052458.1|	1_97	371	332	65	71	245	32.65	109

There was no point picking identical sequnces to align ;)
Default protein alignment from T-Coffee v10.0

t_coffee -infile glucanase.fasta -outfile glucanase_tcoffee.aln
Default protein alignment from Clustal Omega v1.2.1

$ clustalo -i glucanase.fasta -o glucanase_clustalo.aln --outfmt=clustal
Images of the two alignments from Jalview using BLOSUM62 colours
Starting on RBBH and MSA example slides
Crop these images for use in the slides
Some commentary on the RBBH / MSA example
Merge pull request #4 from peterjc/rbbh

RBBH / MSA example