Integrated software tools

[dustman]

I'm trying to find software package that can do all of the following things in transparent or semi-transparent way:
Multiple alignment
Restriction analysis
Sequencing view
Primer design
in silico PCR
Mutagenesis
Virtual cloning
Plasmid maps

UGENE can do most of these things but its focus on 'projects' instead of individual files, plus a number of assorted bugs and bit strange default behaviour drives me mad. Gene Designer can do quite a bit but not everything. EMBOSS is quite complex in its requirements to input.

My normal routine is to pick a gene, already pre-cloned in some sort of plasmid, copy a fragment with PCR, where primers have restriction sites of interest, digest/insert into intermediate/expression construct, purify DNA from selected clones, check, sequence and produce proteins of importance.

I'd like to perform tasks using GUI/semi-graphical interfaces, where main formats used are FASTA/GENBANK. UGENE almost fits this description but its focus on projects leads to huge metafiles where all intermediate (and often redundant) steps are logged and stored.

EMBOSS is probably out of my reach due to its complex installation/usage, or I simple couldn't find gentle enough intro. I wouldn't mind CLI tools tho' (preferably for Windows) if they can help to automate these tasks.

ATM I have FASTA files separately for plasmids, primers, individual sequencings and gene info, and plasmid/gene annotations in GENBANK.

Do you know of something that can do most of this things in uniform, transparent way?

[canalon]

Geneious is not free, but can do most (probably all, but I have not tested) of what you are looking for on most platforms. You can download a free trial version.
In my experience it does a lot of things, is easy to use and install with a clear User interface. Pricey, but well worth it if you need it.

[dustman]

Thank you, Patrick,

Geneious looks interesting, at least after one day trial. Main thing I'm missing is automated plasmid annotations using existing database (or at least I haven't found this feature), a la PlasMapper. I love transparent UniProt/NCBI integration into software.

[JackBean]

What exactly is in silico PCR and virtual cloning?

[dustman]

What exactly is in silico PCR and virtual cloning?

You pick template file, primer(s), specify conditions, run and get a fragment of certain length with expected nucleotide sequence, so you don't need to do it manually <- in silico PCR. Sometimes provides only fragment size(s).

Pick two DNA sequences, specify restriction sites, combine digested fragments and get a new vector <- virtual cloning.

Everything done in a program(s). Main idea of both is to automate so manual tedium can be avoided. Simplifies restriction/PCR analysis of new constructs.