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2ndscore - find the best hairpin anchored at each position.


2ndscore in.fasta > out.hairpins


For every position in the sequence this will output a line:

(score) (start .. end) (left context) (hairpin) (right contenxt)

For positions near the ends of the sequences, the context may be padded with 'x'
characters. If no hairpin can be found, the score will be 'None'.

Multiple fasta files can be given and multiple sequences can be in each fasta file. The
output for each sequence will be separated by a line starting with '>' and containing the
FASTA description of the sequence.

Because the hairpin scores of the plus-strand and minus-strand may differ (due to GU
binding in RNA), by default 2ndscore outputs two sets of hairpins for every sequence: the
FORWARD hairpins and the REVERSE hairpins. All the forward hairpins are output first, and
are identified by having the word 'FORWARD' at the end of the '>' line preceding them.
Similarly, the REVERSE hairpins are listed after a '>' line ending with 'REVERSE'. If you
want to search only one or the other strand, you can use:

--no-fwd Don't print the FORWARD hairpins
--no-rvs Don't print the REVERSE hairpins

You can set the energy function used, just as with transterm with the --gc, --au, --gu,
--mm, --gap options. The --min-loop, --max-loop, and --max-len options are also supported.

The columns for the .bag files are, in order:

1. gene_name
2. terminator_start
3. terminator_end
4. hairpin_score
5. tail_score
6. terminator_sequence

7. terminator_confidence: a combination of the hairpin and tail score that
takes into account how likely such scores are in a random sequence. This
is the main "score" for the terminator and is computed as described in
the paper.

8. APPROXIMATE_distance_from_end_of_gene: The *approximate* number of base
pairs between the end of the gene and the start of the terminator. This
is approximate in several ways: First, (and most important) TransTermHP
doesn't always use the real gene ends. Depending on the options you give
it may trim some off the ends of genes to handle terminators that
partially overlap with genes. Second, where the terminator "begins"
isn't that well defined. This field is intended only for a sanity check
(terminators reported to be the best near the ends of genes shouldn't be
_too far_ from the end of the gene).

TransTermHP uses known gene information for only 3 things: (1) tagging the putative
terminators as either "inside genes" or "intergenic," (2) choosing the background GC-
content percentage to compute the scores, because genes often have different GC content
than the intergenic regions, and (3) producing slightly more readable output. Items (1)
and (3) are not really necessary, and (2) has no effect if your genes have about the same
GC-content as your intergenic regions.

Unfortunately, TransTermHP doesn't yet have a simple option to run without an annotation
file (either .ptt or .coords), and requires at least 2 genes to be present. The solution
is to create fake, small genes that flank each chromosome. To do this, make a fake.coords
file that contains only these two lines:

fakegene1 1 2 chome_id
fakegene2 L-1 L chrom_id

where L is the length of the input sequence and L-1 is 1 less than the length of the input
sequence. "chrom_id" should be the word directly following the ">" in the .fasta file
containing your sequence. (If, for example, your .fasta file began with ">seq1", then
chrom_id = seq1).

This creates a "fake" annotation with two 1-base-long genes flanking the sequence in a
tail-to-tail arrangement: --> <--. TransTermHP can then be run with:

transterm -p expterm.dat sequence.fasta fake.coords

If the G/C content of your intergenic regions is about the same as your genes, then this
won't have too much of an effect on the scores terminators receive. On the other hand,
this use of TransTermHP hasn't been tested much at all, so it's hard to vouch for its

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