Plasmid Mapping Software That Allows Some Command Line Usage

Question

[Anima Mundi]

Hello, I would like you to suggest me a plasmid mapping software (such as VectorNTI, MacVector ecc.) that allows some command line usage; in particular, I would like to graphically visualise cDNA sequences each to aligned to a different reference, so I would need to loop something like (pseudo-Bash code):

suitableprogram -aligntoreference cdna_a.txt cdna_b.txt cdna_c.txt -reference referencefile_1.txt > outputalignmentfile_1

Since every alignment file would be made by very few cDNA subjects, and since the maps (outputalignmentfile_*) are intended to be used by a variety of users, I would like to avoid the use of BAMs, SAMs, GTFs etc.

Thanks in advance.

Answer 1

[Cliff Beall]

EMBOSS will do plasmid mapping and is command-line. It is organized in a bunch of small modules (i.e. alignment and map drawing are separate) so it would probably require some effort to connect up.

[Anima Mundi]

Thanks Cliff; for now, I just put in a separate folder each group made by a reference sequence plus its cDNA so that, when needed, the user can simply open the reference file and align all the remaining files against it (it requires not more than 30 seconds, as it spears the user the search of cDNA variants' files with long names among thousands of files). It is not such an elegant solution, but it was quick and temporary avoided me to introduce new software to the users. In a longer term, I will try to set up an EMBOSS strategy, from the first overview it seems promising.