Read an entry for this sequence, but keep it separate from the others. See the section called The "Entry" in Chapter 1 to see what we mean when we say "entry". The new entry will be marked as active (see the section called The Active Entries in Chapter 1) and will be the new default entry (see the section called The Default Entry in Chapter 1).
This function only reads the feature section of the input file - the sequence (if any) is ignored.
ACT can read these feature files formats:
The output of MSPcrunch. MSPcrunch must be run with the -x or -d flags.
The output of blastall version 2.2.2 or better. blastall must be run with the -m 8 flag which generates one line of information per HSP. Note that currently ACT displays each Blast HSP is a separate feature rather than displaying each BLAST hit as a feature.
Save the entry to the file it came from, unless the entry has been given a new name, in which case the entry is saved to a file with that name. If the entry has no name, ACT will prompt the user for a new name.
Save all the entries that have been loaded on top of this sequence.
Prompt for a file name and then write the translation of the bases of the selected features to that file. The file is written in FASTA format.
Prompt for a file name and then write the translation of the bases of the selected features to that file. The file is written in PIR format (similar to FASTA, but with a * as the last line of each record).
Prompt for a file name and then write the bases of the selection to that file in the selected format. If the selection consists of features (rather than a base range) then the bases of each feature will be written to the file as a separate record. If the selection is a range of bases, then those bases will be written.
Prompt for a number and a file name, then write that many bases upstream of each selected feature to the file in the selected format. For example if the selected feature has a location of "100..200", then asking for 50 upstream will write the bases in the range 50 to 99. Writing upstream bases of a feature on the complementary strand will work in the expected way.
Prompt for a number and a file name, then write that many bases downstream of each selected feature to the file in the selected format.
Prompt for a file name, then write the complete sequence to that file in the selected format.
Prompt for a file name, then write a codon usage table for the selected features. The file in written in the same format as the data at Kazusa codon usage database site. In the output file each codon is followed by it's occurrence count (per thousand) and it's percentage occurrence. (See the section called Add Usage Plots ... to find out how to plot a usage graph).
Open an Artemis edit window for this sequence and features. All changes made in the Artemis window will be immediately visible in the ACT window and vice versa.
See the Artemis manual for more about Artemis.
Close this window.