... Valverde^2.1

jrvalverde@cnb.uam.es

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... can^2.2

You don't have to do this. You can leave EMBOSS where it is and just add the path to the

emboss

directory to your

PATH

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... tree^2.3

FreeBSD users can update their ports tree through a variety of mechanisms. Please see the FreeBSD specific guide produced by Johann for more information

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... installation.^3.1

This location may have been redefined in installations of EMBOSS that have been packaged for specific operating systems. See section 2.6 for further information on OS specific package installations.

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...3.1^3.2

EMBOSS will also look in the

emboss

directory under the EMBOSS source distribution for

emboss.default.template

and install this as

emboss.default

if no existing file is found under the installation directory

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... suit.^3.3

A sample

emboss.default

is located in

emboss/acd

under the source distribution.

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... USA^3.4

Please see the EMBOSS documentation for description of Uniform Sequence Address format

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... appropriate.^3.5

There is one difference to the standard EMBLCD access method in that the database indexes will not allow the generation of exclusive subsections of the combined database. If an ID or accession number is specified that is present in the index then the sequence will be returned irrespective of which database it is in.

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... there.^3.6

Keeping one directory with symbolic links for your BLAST installation will ensure that BLAST continues to function correctly if you set BLASTDB to point to the directory containing the symbolic links. The EMBOSS indices can be placed wherever you wish as long as you remember to run dbiblast with the appropriate options and put an appropriate

indexdir

tag in the DB configuration in your /.embossrc

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... ...^3.7

db is one word

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... ...^3.8

The ID is always taken to be the characters after the last bar (

|

). The previous field is also indexed but ONLY if it looks like an accession number (e.g. AC00001).

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... databases.^3.9

For information on configuring and indexing SRS databases please look at the SRS administrators guide

www/doc/srsadmin.pdf

in your SRS 6 installation

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... FTP.^3.10

ftp://ftp.ebi.ac.uk/pub/databases/rebase

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... FTP.^3.11

ftp://transfac.gbf.de/pub/transfac/ascii/

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... FTP.^3.12

ftp://ftp.ebi.ac.uk/pub/databases/prosite

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... FTP.^3.13

ftp://ftp.ebi.ac.uk/pub/databases/prints

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... FTP.^3.14

ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1

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... FTP.^3.15

ftp://ftp.ebi.ac.uk/pub/databases/cutg/ or ftp://ftp.kazusa.or.jp/pub/codon/current/

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... qualifiers^3.16

See the EMBOSS Quick Guide or the web documentation (or use

wossname -help -verbose

) for an overview of general qualifiers.

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... set.^3.17

You can specifically unset it by using the

-noQUALIFIER

command line option

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... default.^3.18

This can of course be overridden using the

-sformat

and

-osformat

associated qualifiers. See the EMBOSS ACD Syntax documentation or the EMBOSS Quick Guide for more information.

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... appear^5.1

EMBOSS is rebuilt nightly from CVS, tested, and, assuming it passes the compilation tests, the latest version is posted to the EMBOSS FTP server.

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... datafiles^5.2

Assuming of course that you haven't overwritten EMBOSS datafiles with your own to begin with.

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