1BP_FLANKS(1)          User Contributed Perl Documentation         BP_FLANKS(1)
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NAME

6       flanks - finding flanking sequences for a variant in a sequence posi‐
7       tion
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SYNOPSIS

10         flanks --position POS [-p POS ...]  [--flanklen INT]
11                accession ⎪ filename
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DESCRIPTION

14       This script allows you to extract a subsequence around a region of
15       interest from an existing sequence. The output if fasta formatted
16       sequence entry where the header line contains additional information
17       about the location.
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OPTIONS

20       The script takes one unnamed argument which be either a file name in
21       the local file system or a nucleotide sequence accession number.
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23         -p         Position uses simple nucleotide sequence feature table
24         --position notation to define the region of interest, typically a
25                    SNP or microsatellite repeat around which the flanks are
26                    defined.
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28                    There can be more than one position option or you can
29                    give a comma separated list to one position option.
30
31                    The format of a position is:
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33                        [id:] int ⎪ range ⎪ in-between [-]
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35                    The optional id is the name you want to call the new
36                    sequence. If it not given in joins running number to the
37                    entry name with an underscore.
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39                    The position is either a point (e.g. 234), a range (e.g
40                    250..300) or insertion point between nucleotides
41                    (e.g. 234^235)
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43                    If the position is not completely within the source
44                    sequence the output sequence will be truncated and it
45                    will print a warning.
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47                    The optional hyphen [-] at the end of the position
48                    indicates that that you want the retrieved sequence to be
49                    in the opposite strand.
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51         -f         Defaults to 100. This is the length of the nucleotides
52         --flanklen sequence retrieved on both sides of the given position.
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54                    If the source file does not contain
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OUTPUT FORMAT

57       The output is a fasta formatted entry where the description file con‐
58       tains tag=value pairs for information about where in the original
59       sequence the subsequence was taken.
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61       The ID of the fasta entry is the name given at the command line joined
62       by hyphen to the filename or accesion of the source sequence. If no id
63       is given a series of consequtive integers is used.
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65       The tag=value pairs are:
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67       oripos=int
68          position in the source file
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70       strand=1⎪-1
71          strand of the sequence compared to the source sequence
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73       allelepos=int
74          position of the region of interest in the current entry.  The tag is
75          the same as used by dbSNP@NCBI
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77       The sequence highlights the allele variant position by showing it in
78       upper case and rest of the sequence in lower case characters.
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EXAMPLE

81         % flanks ~/seq/ar.embl
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83         >1_/HOME/HEIKKI/SEQ/AR.EMBL oripos=100 strand=1 allelepos=100
84         taataactcagttcttatttgcacctacttcagtggacactgaatttggaaggtggagga
85         ttttgtttttttcttttaagatctgggcatcttttgaatCtacccttcaagtattaagag
86         acagactgtgagcctagcagggcagatcttgtccaccgtgtgtcttcttctgcacgagac
87         tttgaggctgtcagagcgct
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TODO

90       The input files are assumed to be in EMBL format and the sequences are
91       retrieved only from the EMB database. Make this more generic and use
92       the registry.
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94       head1 FEEDBACK
95
96       Mailing Lists
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98       User feedback is an integral part of the evolution of this and other
99       Bioperl modules. Send your comments and suggestions preferably to the
100       Bioperl mailing lists  Your participation is much appreciated.
101
102         bioperl-l@bioperl.org                  - General discussion
103         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
104
105       Reporting Bugs
106
107       Report bugs to the Bioperl bug tracking system to help us keep track
108       the bugs and their resolution.  Bug reports can be submitted via the
109       web:
110
111         http://bugzilla.open-bio.org/
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AUTHOR - Heikki Lehvaslaiho

114       Email:  <heikki-at-bioperl-dot-org>
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118perl v5.8.8                       2007-05-07                      BP_FLANKS(1)