famCircle 0.2.5

famCircle

famCircle 基因家族分析，tandem可视化分析

分析流程

基因组下载以及处理 路线： 前期处理序列比对、共线性扫描、ks计算 ks展示 全基因组 ks展示 block ks展示 circle全基因组共线性展示 line局部共线性绘制 hmmer 隐马尔可夫模型搜索筛选 screen tandem数量分部 断开处： pfam结构域筛选# http://pfam.xfam.org/ α/β筛选# http://cb.csail.mit.edu/cb/paircoil2/ 主程序选择： inner typing 数据格式化 inner绘图 outer typing 数据格式化 outer绘图 part局部tandem绘制

配置文件解释

总体ks分布可视化

run ks ks = ks file vertical = False bins = 100 model = YN00/NG86 savefile = save file (*.png, *.pdf)

基因块ks分布可视化

run Ks_allocation ks = ks file area = 0,2 vertical = False model = YN00/NG86 blockfile = block file blocklength = 6 pvalue = 0.05 savefile = save file (*.png, *.pdf)

共线性可视化

run circle lens = lens file gff = gff file chrolist = Genome name ks = ks file genepairs = genepairs file peripheral = False block = 6 Ks_concern = 0,0.15 bridge = 1 radius = 0.3 savefile = save file (*.png, *.pdf)

基因家族查找

run hmmer pep = pep file# 蛋白质文件 hmmmoldpath = hmm file# 模型地址 format_conversion = Fales# 格式转换 comparison = muscle/clustal# 比对软件 e_value1 = value1# 初筛阈值 e_value2 = value2# 复筛阈值

结构域筛选

α/β筛选

结构域分布情况

run screen domainpath = domain file path lens = lens file gff = gff file chrolist = Genome name series = 25# 串联数 outpath = out file path

文件格式化

run typing domainpath = domain file# 文件路径 domainlist = Genome name# 文件名列表 position = inner/outer# 目标程序格式 savefile = out file# 保存文件

内卷型的tandem可视化

run inner lens = lens file gff = gff file chrolist = Genome name ks = ks file genefamily = famliy file Ks_concern = 0.1,0.2,1.4,1.5# ks分割参数可调 bridge = 0.05# 最远连接 radius = 0.3 peripheral = False savecsv = outer file (.csv) savefile = save file (.png, *.pdf)

放射型的tandem可视化

run outer lens = lens file gff = gff file chrolist = Genome name ks = ks file genepairs = genepairs file Ks_concern = 0,0.15# ks分割参数可调 series = 25# 串联数 clusters = None# 集团参数可调 peripheral = False bridge = 1# 跨区域连线参数可调 radius = 0.3 savecsv = outer file (.csv) savefile = save file (.png, *.pdf)

[circle] lens = lens file gff = gff file species_list = Genome name ks = ks file genepairs = genepairs file block = 6 radius = 0.45 savefile = save file (*.png, *.pdf)

[circle_all] lens = lens file gff = gff file species_list = Genome name blockfile = block file radius = 0.3 savefile = save file (*.png, *.pdf)

[hmmer] pep = pep file cds = cds file hmmmoldpath = hmm file format_conversion = Fales comparison = clustal e_value1 = value1 e_value2 = value2

[inner] lens = lens file gff = gff file chrolist = Genome name ks = ks file genefamily = famliy file Ks_concern = 0,1.5 radius = 0.3 space = 0.005 clusters = True peripheral = False savecsv = outer file (.csv) savefile = save file (.png, *.pdf)

[Ks] cds_file = cds file pep_file = pep file align_software = muscle pairs_file = gene pairs file ks_file = ks result

[Ks_allocation] ks = ks file species_list = specise name area = 0,2.5 model = YN00/NG86 savefile = save file (*.png, *.pdf)

[Ks_block] species_list = specise name ks = ks file area = 0,2.5 model = YN00/NG86 blockfile = block file blocklength = 6 pvalue = 1e-5 savecsv = save csv savefile = save file (*.png, *.pdf)

[line] pairs_file = pairs file gff1 = gff1 file gff2 = gff2 file lens1 = lens1 file lens2 = lens2 file chr1_name = chr1 name chr2_name = chr2 name savefile = savefile(.png,.pdf)

[outer] lens = lens file gff = gff file chrolist = Genome name ks = ks file genefamily = famliy file Ks_concern = 0,0.15 radius = 0.3 space = 0.005 clusters = True peripheral = False savecsv = outer file (.csv) savefile = save file (.png, *.pdf)

[part] lens = lens file gff = gff file chrolist = Genome name ks = ks file genefamily = famliy file Ks_concern = 0,1.5 radius = 0.3 space = 0.005 clusters = True peripheral = False savecsv = outer file (.csv) savefile = save file (.png, *.pdf)

[screen] domainpath = domain file lens = lens file gff = gff file chrolist = Genome name series = 25 outpath = out file

[typing] domainpath = domain file domainlist = Genome name savefile = out file