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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

       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

           --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 accuracy.




       Alex Mestiashvili <>

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