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GBrowse_syn

GBrowse syn

GBrowse syn 安装#

官网: http://gmod.org/wiki/GBrowse_syn
下载安装: https://github.com/GMOD/GBrowse

GBrowse syn 配置#

在安装步骤中最后一步生成的gbrowse.conf文件中找到GBROWSE_CONF设置的路径, 在该路径中找到synteny目录，其中放置配置文件。

此为官方提供的一个教程http://gmod.org/wiki/GBrowse_syn_Tutorial#The_GBrowse_syn_Config_File

配置实例#

  1. 本实例已安装好GBrowse syn, 配置文件存放在/etc/gbrowse/synteny目录中。
  2. 本实例为棉花中的TM-1_WHU与A1_WHU两个基因组的比对。
  3. 首先准备TM-1_WHU与A1_WHU的gff注释文件。
    第七步中配置conf文件中的balloon hover气泡栏需要gff文件中mRNA行有gene Name。
    gff文件头部格式如下： 
    ##gff-version 3
##sequence-region A01 1 112577161
##sequence-region A02 1 104266397
##sequence-region A03 1 105393268
...
  4. 准备TM-1_WHU与A1_WHU的CLUSTALW格式的比对文件
    示例文件: 
    $ zcat rice.aln.gz | head -20

CLUSTAL W(1.81) multiple sequence alignment W(1.81)


rice-3(+)/16598648-16600199      ggaggccggccgtctgccatgcgtgagccagacggggcgggccggagacaggccacgtgg
wild_rice-3(+)/14467855-14469373 gggggccgg------------------------------------agacaggccacgtgg
                                 ** ******                                    ***************


rice-3(+)/16598648-16600199      ccctgccccgggctgttgacccactggcacccctgtcccgggttgtcgccctcctttccc
wild_rice-3(+)/14467855-14469373 ccctgccccgggctgttgacccactggcacccctgtcccgggttgtcgccctcctttccc
                                 ************************************************************


rice-3(+)/16598648-16600199      cgccatgctctaagtttgctcctcttctcgaacttctctctttgattcttcacgtcctct
wild_rice-3(+)/14467855-14469373 cgccatgctctaagtttgctcctcttctcgaacttctctctttgattcttcacgtcctct
                                 ************************************************************


rice-3(+)/16598648-16600199      tggagcctccccttctagctcgatcacgctctgctcttccgcttggaggctggcaaaact
wild_rice-3(+)/14467855-14469373 tggagcctccccttctagctcgatcgcgctctgctcttccgcttggaggctggcaaaact
  5. mysql中创建数据库
    create database TM_1_WHU_VS_A1_WHU;
grant SELECT on TM_1_WHU_VS_A1_WHU.* to 'www-data'@'localhost';

create database TM_1_WHU;
grant SELECT on TM_1_WHU.* to 'www-data'@'localhost';

create database A1_WHU;
grant SELECT on A1_WHU.* to 'www-data'@'localhost';
  6. 导入数据 
    #使用gbrowse中的gbrowse_syn_load_alignments_msa.pl程序导入比对数据
# -u mysql的用户名
# -p mysql的密码
# -d 数据库名
# -c 比对数据文件
path_to_gbrowse/bin/gbrowse_syn_load_alignments_msa.pl -u user -p password -d TM_1_WHU_VS_A1_WHU -v -c TM_1_WHU_VS_A1_WHU.aln

#使用bp_seqfeature_load导入gff注释文件
#-d中的mysql_socket指的是mysql的socket文件存放路径, 没有修改过其路径则不需要填写
bp_seqfeature_load -u user -p password -d dbi:mysql:TM_1_WHU:mysql_socket=/store/db_save/run/mysqld.sock -c -f TM_1_WHU.gff3
bp_seqfeature_load -u user -p password -d dbi:mysql:A1_WHU:mysql_socket=/store/db_save/run/mysqld.sock -c -f A1_WHU.gff3
  7. 在/etc/gbrowse/synteny中创建配置文件
    TM-1_WHU_A1_WHU.synconf: 
    [GENERAL]
description = TM-1_WHU v.s. A1_WHU
# The synteny database
join        = dbi:mysql:database=TM_1_WHU_VS_A1_WHU;host=localhost;user='www-data';mysql_socket=/store/db_save/run/mysqld.sock
#                 symbolic src   config file (".conf")    Description
source_map =      TM_1_WHU           TM_1_WHU             "TM-1_WHU"
                  A1_WHU             A1_WHU               "A1_WHU"

# web site configuration info
tmpimages     = /tmp/gbrowse
imagewidth    = 800
stylesheet    = /static/css/gbrowse/gbrowse_transparent.css

# The extension of species config files
# can also use .syn (the default)
config_extension = conf

# example searches to display
examples = TM_1_WHU A01:95800..145799
           A1_WHU Chr07:90330000..90369999

zoom levels = 5000 10000 25000 50000 100000 200000 400000 1000000

# species-specific databases
[TM_1_WHU]
tracks    = CG CG:TE
color     = cyan

[A1_WHU]
tracks    = CG CG:TE
color     = mediumslateblue
    TM_1_WHU.conf (A1_WHU.conf仿照TM_1_WHU.conf改写): 
    [GENERAL]
description   = TM-1_WHU
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn dbi:mysql:TM_1_WHU:mysql_socket=/store/db_save/run/mysqld.sock

tmpimages   = /tmp/gbrowse

[CG]
label        = 1
description  = 1
feature      = mRNA
category     = Genes
glyph        = processed_transcript
font2color   = blue
height       = 6
key          = mRNA
bgcolor      = sub {
  my $flip = pop->panel->flip;
  my $strand = shift->strand;
  return $strand < 0 ? 'violet' : 'turquoise' if $flip;
  return $strand > 0 ? 'violet' : 'turquoise';
}
balloon hover = $method: $name $ref:$start.. $end

[CG:TE]
label        = 1
description  = 1
feature      = TE
category     = Genes
font2color   = #DEE520
height       = 6
key          = TE
bgcolor      = #DAF409
balloon hover = $method: $name $ref:$start.. $end

# draw genes differently for segments > 100Kb
[CG:100001]
label        = 0
description  = 0
glyph        = generic
strand_arrow = 1
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