Documentation read from 04/17/2019 22:07:27 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_possible_joins.

svr_possible_joins

svr_possible_joins

Given kmer hits on ends of contigs, just group the hits having the same functions to support finding cases in which genes might span contigs.

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Example:

    svr_just_ends < contigs | svr_assign_to_dna_using_figfams | perl svr_possible_joins

would produce something like

ctg7180000000449 10257 10809 Antiadhesin Pls, binding to squamous nasal epithelial cells ctg7180000000549 11391 11799 Antiadhesin Pls, binding to squamous nasal epithelial cells

ctg7180000000282 2306 1937 Arsenate reductase (EC 1.20.4.1) ctg7180000000453 449 848 Arsenate reductase (EC 1.20.4.1)

ctg7180000000282 2697 2326 Arsenic efflux pump protein ctg7180000000452 200959 201954 Arsenic efflux pump protein ctg7180000000453 3 429 Arsenic efflux pump protein ctg7180000000455 1000 1 Arsenic efflux pump protein

ctg7180000000282 1000 850 Chromate transport protein ChrA ctg7180000000282 1834 1699 Chromate transport protein ChrA

. . .

Each line contains a region on a contig that seems to encode a protein. These lines are grouped into two or more that correspond to proteins with the designated function. In some cases (the first and last in the example output above), these are definitely not ends that span contigs. In other cases (the third above), you have groups that need to be resolved.

In any event, before doing directed sequencing to close any of these "gaps", blast the indicated ends against complete non-redundant databases and piece out what it means first.

This is just a simple, fast tool that can supply relevant clues in some cases.

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