Sequence Analysis using tacg V4.6
This form allows you to supply both DNA sequence and (optionally) your own file of Restriction Enzymesor other IUPAC patterns in GCG format  (or slightly modified for more functionality) for Restriction Enzyme Mapping and Analysis, using Harry Mangalam's tacg 4.6 program as the analysis engine.
You should be able to see the ends of the thick grey horizontal line below in your window
Sequence Entry
--EITHER-- Paste in the RAW sequence in the window below..       Notes on format
[Optional Output Label for pasted-in sequence]
--OR-- use the file browser below...
Use the file browser below to upload a DNA sequence file (<500,000 characters) to send:
(Output will be labeled with the file name.)


    Force sequence file to be Read as 'raw'. (only numbers, spaces, and sequence)
--OR-- Insert valid Genbank Accession Numbers or IDs
in the box below and they'll be retrieved from NCBI (slow - several seconds).
Valid Genbank Accession Numbers:

SubSequence Selection and Numbering Options
The sequence should be analyzed from bases:
to  (use "END" to indicate end; integers for other endpoints.)
The (sub)sequence should be analyzed as: Linear  Circular 
Sequence numbering should start from:
(Only for Linear Map; Sites are numbered starting from 1.)



Restriction Enzyme Selection
Select the Restriction Enzymes either By Characteristic or Explicitly
Filtering options below left apply to entire REBASE files (yours or mine), but not to EXPLICITLY picked enzymes to right.
  Search for possible SILENT Sites (supercedes all other selections and forces Linear Map Mode).
Number of hits:     Minimum:     Maximum:     Affects BOTH columns of selections
Select By Characteristic Select Explicitly
This side is the default. This side is selected if ANY names are selected
Overhang
Dam Sensitive
Dcm Sensitive
Magnitude of Recognition Sequence:
  base pairs or greater.
Cost
Selections filtered from from the
 
--OR----------

from YOUR uploaded GCG-formatted REBASE file,
using the file browser below.
Uploads supercede the menu selection.
(To (de)select multiples:   Mac - Cmd+Click
Windows - Ctrl+Click   Unix - Click)
  Simulate multiple digestion.



Output Format
The output should be wide, in  Regular Small tiny   font.  Suggestions
NB: Choosing the VERY wide option makes most of the output stream out in a single line.

Sort Output by # Hits, Names  (DNA Strider-style)
For debugging strange or absent results:
Show me the tacg command line that generated these results.
Show me ERRORs from tacg.



Analyses
  Summary Table (Absent Sites, # of sites for each Pattern)
GCG-like Ladder Map (req >100 b to be useful)
  Pseudo Gel Map  LOW cutoff at bp; HIGH cutoff at bp.
Table of Hit Sites
Table of Fragments Listed by:
  Stream out Open Reading Frames of greater than  Amino Acids
in frames 1 2 3 4 5 6
Print the EXTENDED ORF info.
Print the ORF sequence UNWRAPPED (1 line output).
Print ORF map and MET / STOP map .
Entire Linear Map Long, but required for Co-Translation below.
Only print top strand No tic marks Print Map even if No Hits
Linear Co-Translation: in frame(s), with a   letter code,
using  Codon Usage.
Generate Circular Plasmid Map    Notes on Pasmid Maps
Convert native Postscript to PDF (smaller file)