| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| ACRE1.py | 2013-12-17 | 3.2 kB | |
| ACRE_README.txt | 2013-12-17 | 1.6 kB | |
| grassregions.fasta | 2013-07-25 | 4.2 kB | |
| Totals: 3 Items | 9.0 kB | 0 | |
################################################### # Anchored Conserved Region Extension version1.0 # # # # Bill Wysocki 2013, wwysoc2@gmail.com # ################################################### What it does: ACRE has been designed to efficiently assemble plastomes by locating contigs containing short conserved regions and concatenating contigs when perfect overlap is found in adjacent conserved regions. It has been tested extensively on grass plastomes but can be applied to sequences with any amount of conserved regions. Grass plastome conserved regions were identified using an intrafamilial alignment of 75 full plastomes. ACRE takes a series of user-provided sequences (the region file) and queries the regions (and their reverse-complement) to find a perfect match within a contig file. These contigs are then concatenated when perfect overlap is located between two adjacent contigs with a minimum amount of overlap set by the user. How to use it: ACRE requires both Python 2.7 and the BioPython package. To run ACRE, simply type: python ACRE1.py [contig file] [region file] [overlap] contig file: The file containing the sequences you wish to assemble. This file is required to be in FASTA format. region file: The file containing the short conserved regions in the order in which they appear in your sequence. This file is required to be in FASTA format. overlap: An integer that denotes the required amount of perfect overlap (in base pairs) that is required for ACRE to automatically concatenate two adjacent contigs.
