Software
Pipeline Scripts
Notes:
SmartScreener: Screens nucleotide sequences in tab-delimited format for SMART primer sequence and converts to 'n's. Requires a primer file to work.
Download: SmartScreener.exe, SmartScreener.pl, PrimerFile.txt

QualMod: Modify or trim tab-delimited quality scores and nucleotide sequences. Includes multiple quality filter parameter settings.
v1.01. bug fix
Download: QualMod.exe, QualMod.pl
CreateIndex_Uniprot: Create index and meta-index files for Uniprot flat files (e.g. Uniprot.dat) for fast retrieval of annotations.
v1.2. minor bug fixes
Download: CreateIndex_Uniprot.exe, CreateIndex_Uniprot.pl
IndexedAnnotationRetrieval: Retrieves available annotations from an indexed Uniprot flat file created with CreateIndex_Uniprot.
v1.5. added some output customization options. added Pfam field to output
Download: IndexedAnnotationRetrieval.exe, IndexedAnnotationRetrieval.pl
BlastRowFilter: Filters tab-delimited blast output for top query and top query/subject pairs, as well as bitscore. Option to use exclusion keywords to filter for "best" blast annotation.
v1.10. added annotation filter mode
Download: BlastRowFilter.exe, BlastRowFilter.pl
BlastColumnFilter: Filters tab-delimited multi-query column blast tables for best blast query per row.
v1.10. compatible with AceParser1.33 and SNPHunter2.21.
Download: BlastColumnFilter.exe, BlastColumnFilter.pl
DB_UploadFiles: Upload sequence, blast, and annotation files to a MySQL database using a normalized table format.
Download: DB_UploadFiles.exe, DB_UploadFiles.pl
DB_DownloadFiles: Download data from a MySQL database using various methods (e.g. keyword search).
Download: DB_DownloadFiles.exe, DB_DownloadFiles.pl
AdapterSearch: Removes bar-coded adapter/primer sequence and tags EST titles for population specific assemblies.
Download: AdapterSearch.exe, AdapterSearch.pl
>These perl scripts are designed to be run from the Windows command-prompt (Vista/7) and have standard Unix/DOS-like options functunality (e.g. C:>script1.exe -i input.txt -o output.txt etc.).

>Both pre-packaged executables (exe) and code (pl) are available for most of the scripts. Executables are optimized for 64-bit Windows and may or may not function on 32-bit systems.

>All scripts include a help option (e.g. C:>script1.exe -h) for a general description of function followed by option list.