The purpose of this repository is to describe a simple script of KEGG annotation of AA sequence files First, deploy the KOBAS and Uniprot databses for blast, usearch, and diamond Uniprot/Swissprot cd /data/DATABASES mkdir UNIPROT cd UNIPROT wget ftp://ftp.uniprot.org/pub/databases/uniprot/cur...
Pinus halepensis__KEGG_annotationPinosio, SaraGonzálezMartínez, Santiago CBagnoli, FrancescaCattonaro, FedericaGrivet, DelphineMarroni, FabioLorenzo, ZaidaPausas, Juli GVerdú, MiguelVendramin, Giovanni G
答:以KEGG的注释结果为例:可查找结果文件7-FunctionAnnotation/1.KEGG/Unigenes.KEGG.tax.xls,在其中找到关注的功能已经对应的Gene_ID,返回到5-TaxAnnotation/2.Tables/gene.taxonomy.xls 中使用Gene_ID搜索找到对应的物种名称。Q2:如何查找显著差异基因的具体序列?答:先根据差异分析结果挑选出感兴趣的KO号,根据KO...
KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an integrated database resource for biological interpretation of genome sequences and other high-throughput data. Molecular functions of genes and proteins are associated with ortholog groups an
BMC Genomics 2013, 14:509 http://www.biomedcentral.com/1471-2164/14/509 DATABASE Open Access KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome Walter C Dunlap1,2, Antonio Starcevic4, ...
KEGG数据库没有倒闭,Y叔的clusterProfiler包也问题不大。仅仅是因为R语言里面的下载文件的函数的协议需要注意,这两个函数两个下载函数(utils:download.file和downloader:.download),都太底层了。初学者确实不容易找到问题所在。 道阻且长,行则将至 行而不辍,未来可期...
importosimportjsonimportreclassKOParser(object):def__init__(self,map):self.map=mapdefjson_parser(self):# check the existance of json fileifos.path.exists(self.map):withopen(self.map,'r')asf:ko_list=[]# convert json to dictmap_dict=json.load(f)# print(type(map_dict)) dictmaps=map...
KEGG annotation of DEGs among different tissues of paper mulberry.Peng XianjunTeng LinhongWang XiaomanWang YuchengShen Shihua
gene annotationpathway mappingKAASKEGG is a database resource (http://www.genome.jp/kegg/) that provides all knowledge about genomes and their relationships to biological systems such as cells and whole organisms as well as their interactions with the environment. KEGG is categorized in terms of ...
gene annotationpathway mappingKAASKEGG is a database resource ( http://www.genome.jp/kegg/ ) that provides all knowledge about genomes and their relationships to biological systems such as cells and whole organisms as well as their interactions with the environment. KEGG is categorized in terms ...