nuget server logo nuget api documents
↑

API Docs / SMRUCC.genomics.Interops.NCBI.Extensions

SMRUCC.genomics.Interops.NCBI.Extensions 1.0.9753.40023.

Namespaces 26 Types 74 Members 574

01 Namespaces

SMRUCC.genomics.Interops.NCBI.Extensions

TypeSummary Members
DiamondAnnotation 代表 DIAMOND BLASTP 结果文件 (.m8) 中的一行记录 12
DiamondM8Parser 用于解析 DIAMOND .m8 格式文件的工具类 2
Extensions 1
TermStreamAssignment 2

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Application

TypeSummary Members
Paralog 1

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Application.BBH

TypeSummary Members
BBHParser BBH解析的时候，是不会区分方向的，所以只要保证编号是一致的就会解析出结果，这个不需要担心 10
BestHit A single direction best hit. 3
BHR BHR(Bi-directional hit rate) http://www.genome.jp/tools/kaas/help.html 把要注释的genome作为query，和KEGG数据库中的reference进行blast比对，输出的结果（E>10）称为 homolog。 同时把reference作为query，把genome作为r… 4
BHRHit 1
BiDirectionalBesthit Best hit result from the binary direction blastp result. 5
KOAssignmentCandidate 用于存储一个查询基因的KO分配候选 4
KOAssignmentScore KEGG KAAS Assignment Score (S_KO) 计算模块 7
Levels The blast result alignment identify levels 8

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Application.BBH.Abstract

TypeSummary Members
BBHIndex 可以使用这个对象来表述I_BlastQueryHit的所有派生类 3
Extensions 1
I_BlastQueryHit I_BlastQueryHit.QueryName and I_BlastQueryHit.HitName 5

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Application.BBH.BiDirectionalBesthit

TypeSummary Members
GetDescriptionHandle Get gene function description from the specific locus_tag 3

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Application.NtMapping

TypeSummary Members
BlastnMapping Blastn Mapping for fastaq 11
MapsAPI 9

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput

TypeSummary Members
IBlastOutput Blast程序结果对外输出的统一接口类型对象 6

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput.BlastPlus

TypeSummary Members
BlastnHit 2
BlastpOutputReader 4
FragmentHit 7
ParameterSummary 13
Parser 17
Query 12
SubjectHit 9
v228 2.2.28版本的BLAST+程序的日志输出文件 12

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput.BlastPlus.BlastX

TypeSummary Members
Extensions Extensions API for blastX output table 1
OutputReader 4
v228_BlastX The output result data model of the blastx output text file. 1

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput.BlastPlus.BlastX.Components

TypeSummary Members
HitFragment 7
Query The blastx query input result data. 4
Subject The hits result in target protein sequence database. 5

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput.BlastPlus.Parser

TypeSummary Members
ReaderTypes + BLASTP + BLASTN + BLASTX 3

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput.ComponentModel

TypeSummary Members
BlastXScore 4
HitSegment 表示一个Query和Subject匹配上的序列片段相对应的位置，即HSP高分区片段 5
Parameter 11
Score Query和Subject之间的比对得分 17
Segment 匹配上的序列片段 0

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput.Views

TypeSummary Members
Overview 方便程序调试的一个对象数据结构 1

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput.XmlFile

TypeSummary Members
BlastOutput 11

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.BLASTOutput.XmlFile.Hits

TypeSummary Members
Hit 11

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.InteropService

TypeSummary Members
Executable 5
InitializeMethods 4
InitializeParameter 对本地BLAST外部命令的初始化参数 4
InteropService InteropService to the local blast program.(对本地BLAST程序的中间服务) 8
LocalBlastProgramGroup 7
Operation 通用化操作 8

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.InteropService.InteropService

TypeSummary Members
AlignmentViewOptions Alignment view options.(比对输出视图的选项) 24

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Programs

TypeSummary Members
BLASTPlus The <space> char can not exists in the input fasta file path, or blast+ program will run into an error. 13
LocalBLAST 52

SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Programs.CLIArgumentsBuilder

TypeSummary Members
BlastnOptionalArguments 44
BlastpOptionalArguments 41

SMRUCC.genomics.Interops.NCBI.Extensions.NCBIBlastResult

TypeSummary Members
AlignmentTableParser 6
BBHMetaAPI SpeciesBesthit -> AlignmentTable 1

SMRUCC.genomics.Interops.NCBI.Extensions.NCBIBlastResult.WebBlast

File parser for alignment text output from NCBI web application.

TypeSummary Members
AlignmentTable 10
Extensions 4
HitRecord 在目标基因组之上的blast hit的结果 19
HitTableParser 从NCBI网站之中下载的比对结果的表格文本文件之中进行数据的解析操作 3

SMRUCC.genomics.Interops.NCBI.Extensions.Pipeline

The functional annotation analysis pipeline based on the ncbi localblast+ toolkit

TypeSummary Members
Extensions 2
GenomeVector 基因组代谢酶注释结果 8
KOAssignment 4
RankTerm 2

SMRUCC.genomics.Interops.NCBI.Extensions.Pipeline.COG

TypeSummary Members
COG2014 ftp://ftp.ncbi.nih.gov/pub/COG/COG2020/data 1
COGsUtils Cog分类操作 2
MGACOG COG output data from http://weizhong-lab.ucsd.edu/metagenomic-analysis/server/ 0
MyvaCOG Protein cog category using myva database. 3

SMRUCC.genomics.Interops.NCBI.Extensions.Pipeline.COG.Whog

TypeSummary Members
Assigner 1
WhogRepository Cog Category 7

SMRUCC.genomics.Interops.NCBI.Extensions.Tasks.Models

TypeSummary Members
Hit 和Query的一个比对结果 8
HitCollection A collection of hits for the target query protein. 9
SpeciesBesthit 元数据Xml文件 15

SMRUCC.genomics.Interops.NCBI.Extensions.Web

TypeSummary Members
KeggSSDB KEGG SSDB API 0