Synteny comparison

Method

L. ferriphilum ML-04 and L. ferriphilum YSK, two strains having complete genome were selected for comparison. Their sequences were downloaded and decompressed. BLAST was used to make a database of my assembly and then produce crunch files for ACT to view comparison.
Command:

makeblastdb -in lfts.fasta -out lfts -dbtype nucl
blastn -query ml04.fna -out lfts_ml04.crunch -db lfts -outfmt 6
blastn -query ysk.fna -out lfts_ysk.crunch -db lfts -outfmt 6

• -outfmt 6 is required for ACT

Results and discussion

The sequence in the middle is my contigs.fasta. Considering the circular feature of the genome, the first contig aligns well with both ML-04 and YSK. The size of contig 1 is larger and a new region is presented.

Q & A

Homology search

1. How relevant is the output format that you choose?

• Different output formats are for different usages. Different software require different format to parse. As said above, ACT requires format 6 of BLAST+.

2. How do the resulting hits vary when you change the minimum e-value?

• E-value represents the number of hits expected to see by chance when searching a database of a particular size. The lower the e-value, the more significant the match is. Decreasing minimum e-values generates less resulting hits.

3. How is the alignment score calculated?

• It is calculated by summing the substitution score (base on substitution matrix) and gap scores (opening and extension penalties).

4. How important is the number of threads when you blast against a database, or against a particular sequence?

• Increasing the number of threads to utilize parallel computation will increase the speed of search.