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When I attempt to call it using system I get this response.

'blast2seq.exe' is not recognized as an internal or external command,
operable program or batch file.

what have I done wrong in the...

The only languages I have experience with are C and java, I have no idea how to write *.bat files. system("command") will probably work just fine.

The arguments list for the blast program are as follows (given when running the program without arguments)
D:\UMDNJ\BLAST\bin>bl2seq.exe

bl2seq 2.2.18 arguments:

-i First sequence [File...

I do not believe that the BLAST software (which does not have a built in gui) was equipped to handle batch inputs. It usually only runs a single input. (blast usually compares one DNA strand against...

I'm trying to write a program that takes information from a text file and uses it to provide arguments to another executable file.

I want to use a BLAST executable to compare several DNA sequence...