BoM / KJV Bible BLAST Sequence Alignment

This project uses the BLAST+ genetic sequence alignment tool to find likely biblical sources for every sentence in the Book of Mormon.

Installation

Install BLAST+ on Mac OS:

brew install homebrew/science/blast

Install ruby gems:

bundle install

Note: You'll need ruby 2.3 and bundler installed.

Prepare the King James Bible FASTA file

cd data
bundle exec ruby ../kjv.rb >kjv.fasta

Prepare the Book of Mormon FASTA file

cd data
bundle exec ruby ../bom.rb >bom.fasta

Create the BLAST database

cd data
makeblastdb -in kjv.fasta -parse_seqids -dbtype prot

Search

Search for a specific index/verse:

$ blastdbcmd -db kjv.fasta -entry GENESIS-1-1-A
>GENESIS-1-1-A 
INTHEBEGINNINGGODCREATEDTHEHEAVENANDTHEEARTH

Here's a sample query file, e.g. query.faa:

>TEST-1
DARKNESS WAS AN INTERESTING THING
>TEST-2
DID THE FIRMAMENT ALWAYS LOOK LIKE THAT

Then search for closest matches:

cd data
$ blastp -query query.fasta -db kjv.fasta

Find Book of Mormon Sequences

cd data
$ blastp -query bom.fasta -db kjv.fasta -culling_limit 5 >results.txt

The results will show signficant alignments (if any) and the character-aligned best matches.

Sample Results

Query= 1 NEPHI-1-3-B

Length=25
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

1-CORINTHIANS-16-21-A  unnamed protein product                        35.8    3e-06
PHILEMON-1-19-A  unnamed protein product                              37.0    4e-06
1-SAMUEL-25-33-A  unnamed protein product                             37.0    4e-06
GALATIANS-6-11-A  unnamed protein product                             33.1    6e-05
2-CHRONICLES-6-15-B  unnamed protein product                          27.7    0.009
2-TIMOTHY-4-11-A  unnamed protein product                             23.5    0.21 

>GALATIANS-6-11-A unnamed protein product
Length=54

 Score = 33.1 bits (74),  Expect = 6e-05, Method: Compositional matrix adjust.
 Identities = 15/15 (100%), Positives = 15/15 (100%), Gaps = 0/15 (0%)

Query  11  WITHMINEOWNHAND  25
           WITHMINEOWNHAND
Sbjct  40  WITHMINEOWNHAND  54

The complete output (results.txt) is about 45 MB.

Misc

Handy reference for BLAST to BLAST+: http://www.vicbioinformatics.com/documents/Quick_Start_Guide_BLAST_to_BLAST+.pdf

Index sequences cannot contain ":" so, for biblical verse refs, use this format: BOOK-CHAPTER-VERSE-PART, e.g. GENESIS-1-1-A

Spaces appear to be automatically removed from FASTA files.