BLAST-based, synteny-aware (protein) sequence searching.

synteBLAST is a search pipeline designed to find co-linear (syntenic) blocks of genes that are similar to a query block in both sequence and arrangement on the genome.

Prokaryotes often utilize blocks of cotranscribed genes called operons to carry out similar functional tasks. A texbook example of operons (literally) is the lac operon of Escherichia coli.

synteBLAST was written by Timothy Driscoll at West Virginia University, Morgantown, WV USA. The concept for a synteny-aware search algorithm arose from discussions and work with numerous other researchers, most notably Joseph J. Gillespie (University of Maryland) and Victoria Verhoeve (West Virginia University).

Run the synteblast wrapper shell script, passing it a fasta file that contains the sequences for the colinear block, in the desired order, to use as query:

synteblast -i INPUT_BLOCK.faa

synteblast will produce four output files, all with the prefix synteblast_out. The final results are written to a file called synteblast_out.3.ranked; this is a tab-delimited file containing all matches to the query block in order (best matches at the top). This file can be imported or copied directly into an app like Excel.

synteblast also accepts several optional arguments that you can use to customize your results. A complete list can be found by running synteblast -h.

synteblast -i INPUT_BLOCK.faa [-o OUTBASE] [-e FLOAT] [-p FLOAT] [-c FLOAT] [-f STRING] [-m STRING] [-F]

-i <filepath>

REQUIRED Path to a protein fasta file containing the ordered query sequences.

-o <string>

OPTIONAL String to use as the prefix to project output file names.

-e <float>

OPTIONAL Value to use as the maximum e-value for sequence matches. Used during the initial remote blast query. [default: 0.001]

-p <float>

OPTIONAL Value (0-100) to use as the minimum percent identity between match and query. Used during the thresholding step. [default: 40]

-c <float>

OPTIONAL Value (0-100) to use as the minimum percent coverage across the query. Used during the thresholding step. [default: 60]

-f <string>

OPTIONAL Entrez string to filter the initial remote blast query. [default: bacteria[orgn] AND "srcdb refseq"[Properties]]

-m <string>

OPTIONAL Scoring matrix to use for the initial remote blast query. [default: BLOSUM45]

-F

OPTIONAL Set this flag to force synteblast to write over an existing blast file. By default, the initial blast query will not be run if an output file of the same name already exists, since this is almost always a very time-consuming step. [default: false]

synteBLAST is released under the GNU GPL v3 license. Please see the file LICENSE included in the top-level synteblast directory of every release.