Affiliated Utilities

BLAST/data preparation

• Clean FASTA sequence by removing extra whites spaces, digits or symbols such as ":", ".", "|" etc.
• Remove batch data from FASTA file
• Create unique BLAST query data set

BLAST

• 1 to 1 BLAST
• Many to many BLAST
• Many to NCBI db BLAST
• BLAST results parsing & filtering (current for DNA only)

Batch Sim4

• Batch cDNA align to 1 gDNA (Sim4)

Genbank, gb-header, feature table and GFF format conversion and manipulation

• Create Genbank format feature header
• Extract gb-header from Genbank
• Merge multiple gb-header files
• Cleanup gb-header file
• Merge gb-header with sequence data
• Conversion between standard Genbank format gb-header and VNTI format gb-header
• Genbank feature table extraction
• Format Genbank format sequence body
• Feature-related sequence extraction
• Convert Genbank format into GFF
• Convert DNannotator feature table into GFF
• Remove batch features from gb-header or feature table
• Search for duplicated features

Others

• Screen primer for repeats

• Convert Mac format to Unix format

• Remove HTML tags from a .html file and generate a plain text file

utilities would help you to do some batch data processing not limited with DNannotator.