OnWorks favicon

bp_flanksp - Online in the Cloud

Run bp_flanksp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bp_flanksp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



bp_flanks - finding flanking sequences for a variant in a sequence position


bp_flanks --position POS [-p POS ...] [--flanklen INT]
accession | filename


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


The script takes one unnamed argument which be either a file name in the local file system
or a nucleotide sequence accession number.

-p Position uses simple nucleotide sequence feature table
--position notation to define the region of interest, typically a
SNP or microsatellite repeat around which the flanks are

There can be more than one position option or you can
give a comma separated list to one position option.

The format of a position is:

[id:] int | range | in-between [-]

The optional id is the name you want to call the new
sequence. If it not given in joins running number to the
entry name with an underscore.

The position is either a point (e.g. 234), a range (e.g
250..300) or insertion point between nucleotides
(e.g. 234^235)

If the position is not completely within the source
sequence the output sequence will be truncated and it
will print a warning.

The optional hyphen [-] at the end of the position
indicates that that you want the retrieved sequence to be
in the opposite strand.

-f Defaults to 100. This is the length of the nucleotides
--flanklen sequence retrieved on both sides of the given position.

If the source file does not contain


The output is a fasta formatted entry where the description file contains tag=value pairs
for information about where in the original sequence the subsequence was taken.

The ID of the fasta entry is the name given at the command line joined by hyphen to the
filename or accesion of the source sequence. If no id is given a series of consequtive
integers is used.

The tag=value pairs are:

position in the source file

strand of the sequence compared to the source sequence

position of the region of interest in the current entry. The tag is the same as used

The sequence highlights the allele variant position by showing it in upper case and rest
of the sequence in lower case characters.


% bp_flanks ~/seq/ar.embl

>1_/HOME/HEIKKI/SEQ/AR.EMBL oripos=100 strand=1 allelepos=100


The input files are assumed to be in EMBL format and the sequences are retrieved only from
the EMB database. Make this more generic and use the registry.


Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to the Bioperl mailing lists Your participation
is much appreciated.

[email protected] - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
resolution. Bug reports can be submitted via the web:


AUTHOR - Heikki Lehvaslaiho

Email: <heikki-at-bioperl-dot-org>

Use bp_flanksp online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    This repository is no longer maintained
    and is kept for archival purposes. See
    https://invent.kde.org/sdk/kdiff3 for
    the newest code and
    Download KDiff3
  • 2
    USBLoaderGX is a GUI for
    Waninkoko's USB Loader, based on
    libwiigui. It allows listing and
    launching Wii games, Gamecube games and
    homebrew on Wii and WiiU...
    Download USBLoaderGX
  • 3
    Firebird RDBMS offers ANSI SQL features
    & runs on Linux, Windows &
    several Unix platforms. Features
    excellent concurrency & performance
    & power...
    Download Firebird
  • 4
    KompoZer is a wysiwyg HTML editor using
    the Mozilla Composer codebase. As
    Nvu's development has been stopped
    in 2005, KompoZer fixes many bugs and
    adds a f...
    Download KompoZer
  • 5
    Free Manga Downloader
    Free Manga Downloader
    The Free Manga Downloader (FMD) is an
    open source application written in
    Object-Pascal for managing and
    downloading manga from various websites.
    This is a mirr...
    Download Free Manga Downloader
  • 6
    UNetbootin allows you to create bootable
    Live USB drives for Ubuntu, Fedora, and
    other Linux distributions without
    burning a CD. It runs on Windows, Linux,
    and ...
    Download UNetbootin
  • 7
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM is an easy to use
    ERP and CRM open source software package
    (run with a web php server or as
    standalone software) for businesses,
    Download Dolibarr ERP - CRM
  • More »

Linux commands