ProRecon is a lightweight Java library that is designed to RECONstruct PROteins consider different mutations.
Detailed presentation can be found here:
Pdf - https://drive.google.com/open?id=0B1g2jSBV2uqrZWljM3c4S1oxbGc
Video - https://drive.google.com/open?id=0B1V1JjzgsVlLTjk4UHlrcHl3NmM
For now example can be found in temporary Main class or you can use jar with dependencies:
java -cp prorecon.jar com.epam.prorecon.Main "dmel-all-chromosome-r606.fasta" "agnX1.model.2.snp-indels.vcf" "dmel-all-r6.06.LIMK1.gtf" "X" 12584385 12592193
where "dmel-all-chromosome-r606.fasta" is file with original sequence,
"agnX1.model.2.snp-indels.vcf" is file with mutations list,
"dmel-all-r6.06.LIMK1.gtf" is file with exons positions indexes,
"X" is chromosome name,
12584385 is DNA sequence start index,
12592193 is DNA sequence end index.
ProRecon is free software: You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 of the License.
This program is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should receive a copy of the GNU General Public License along with this program. If you did not, please see http://www.gnu.org/licenses/.