GAPMap Installation Guide

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13 Δεκ 2013 (πριν από 3 χρόνια και 10 μήνες)

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1

GAPMap Installation Guide


Lei

Zhang

2007
-
12
-
4

Email:
zhanglei@chgc.sh.cn



Abstract

This document describes how to install use GAPMap,

G
enome
A
nnotation and
P
athway
M
apping on
variant Linux Operating systems


Content


1. Introduce

................................
................................
................................
................................
.......

1

2. Install Perl and GD package

................................
................................
................................
..........

1

3. Preparing
datasets

................................
................................
................................
.........................

1

4. Run the Program

................................
................................
................................
...........................

2



1. Introduce

GAPMap,

G
enome
A
nnotation and
P
athway
M
apping
, is written purely in perl with the GD
package based on KEGG and NC
BI Taxonomy database. It is available for all Linux
environments. The Users are required to install GD package and to prepare essential
datasets which we provide in our
website
b
efore running the GAPMap software.

(
http://www.chgc.sh.cn/e
n/software/gapmap/download.html
)


2. Install Perl and
GD packag
e

The Software was tested with perl version 5.8.8 and GD version 2.3.5. detailed install
refernce can be obtained in the Perl and GD install

package.

The systems with
minimums

memory of 2G are
recommend
ed.

3. Preparing datasets

The software requires strict directory tree structure which we have provided in the
compressed file

data.tar.gz

.
The datasets and directory are listed below.

(data.tar.
gz,
http://www.chgc.sh.cn/en/software/gapmap/download/data.tar.gz
).



kegg

The blast result with KEGG genes as query

should

be put
in this directory
. The

Blast
result
should

inclu
de o
riginal

blast result and parsed blast
result (
The parsing
Program also provide in our website).




ko


2


The directory contains the KEGG refernce pathway data which describe
s

the KO,
compound and their coordinate
information



ftp://ftp.genome.jp/pub/kegg/pathway/ko



map

The directory contains the KEGG refernce pathway image files with GIF fileformat
and
transformed PNG fileformat.



compound

KEGG compound file from KEGG LIGAND database.

ftp://ftp.genome.jp/pub/kegg/ligand/compound



reaction

KEGG
reaction
file from KEGG LIGAND database.

ftp://ftp.genome.jp/pub/kegg/ligand/reactio
n



CompoundSubPathway.lst

The parsed sub
-
pathway list from the reconstructed metabolic network.



ko.list

KEGG ko file from KEGG ORTHOLOGY (KO) database

ftp://ftp.genome.jp/pub/kegg/genes/



gene_ko.lst

Gene
_ko.lst can be obtain from KEGG linkdb database:

ftp://ftp.genome.jp/pub/kegg/linkdb/genes


Sometimes, in order to keep accordance with the KO file, we may parse the gene

ko
relationship direct
ly though the KO file.



ko2genespecies.lst

The file describes the relationship between KEGG KO number and all genes in a
certain species with such format below.

ko:K00001

hsa:124

hsa:125

hsa:126

hsa:127

hsa:128

hsa:130

hsa:131

hsa:137872




map_title.tab

T
he KEGG pathway ko information.

I
n the main
d
irectory
, there

should be the blast result with o
riginal

and parsed result.
A
nd
the genes and protein fasta
sequence

also should exist in this directory.

4
.
Run
the

Program

Th
e
re

are 8
parameter
s which are desc
ribed below.

W
hen you run the program you should input the
command:

P
erl
GAPMap.pl
-
D
-
AA
-
NA
-
Q0
-
Q1
-
B
-
R0
-
E
-
T

[options]:


-
D <OUTPUT Dir>


-
AA <Amino acide Fasta sequence>


-
AA <Nucleotideacide Fasta sequence>


-
Q0 <query Parsed Result>


-
Q1 <query non Parsed Result>


-
B

<blast reslut dir>


-
R0 <Reverse Blast Parsed Reselst>


-
E

<Hit
-
EVALUE>


-
T

<Species Tree Distance>


3

4
.
The Flow cha
r
t

of
the system