蛋白序列GO号注释及问题
#=============================== 版本1 ===============================================
InterProScan的三种使用方法
Interproscan,通过蛋白质结构域和功能位点数据库预测蛋白质功能。是EBI开发的一个集成了蛋白质家族、结构域和功能位点的非冗余数据库。Interproscan整合了一些使用最普及的一些数据库，并应用于功能未知的蛋白进行Interpro注释和GO注释。
以下介绍3中interpro注释的方法：
三、本地化的InterProScan注释
3.1 本地化的InterProScan安装与配置
3.1.1 从ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan下载以下5个文件：
RELEASE/latest/iprscan_v4.8.tar.gz BIN/4.x/iprscan_bin4.x_[PLATFORM].tar.gz DATA/iprscan_DATA_[LATESTDATAVERSION].tar.gz DATA/iprscan_PTHR_DATA_[LATESTDATAVERSION].tar.gz DATA/iprscan_MATCH_DATA_[LATESTDATAVERSION].tar.gz
3.1.2 将5个文件解压到一个文件夹中，然后运行其中的文件Config.pl，来对InterProScan进行配置。
3.1.3 配置的过程中，若选择进行本地web配置，则修改本地www服务的配置文件，以能进行本地化网页版的运行。
3.2 本地化InterProScan的使用。
3.2.1 命令行运行iprscan的方法：
$bin/iprscan -cli -iprlookup -goterms -format xml -i test.fasta -o test.out
# help
http://www.chenlianfu.com/?tag=iprscan
该模块中XML::Parser XML::Parser::Expat 这两个模块，后一个必须先安装，后续一个接着安装，由于是C层面的模块，需要安装一些东西
Expat must be installed prior to building XML::Parser and I can't find it in the standard library directories. Install 'expat-devel' (or 'libexpat1-dev') package
小提示： （root或者sudo权限） yum 或者 apt-get install expat-devel （具体版本具体办）
#============================================== 版本2 =============================================
https://github.com/ebi-pf-team/interproscan/wiki 原文链接
第一步： 环境配置
Software requirements:
- 64-bit Linux
- Perl (default on most Linux distributions)
- Python 2.7.x only
- Oracle's Java JDK/JRE version 8 (required by InterProScan 5.17-56.0 onwards). Earlier InterProScan release versions required Java 6 (version 6u4 and above) or Java 7.
- Environment variables set
- $JAVA_HOME should point to the location of the JVM
$JAVA_HOME/bin should be added to the $PATH
第二步： 数据下载
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.27-66.0/interproscan-5.27-66.0-64-bit.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.27-66.0/interproscan-5.27-66.0-64-bit.tar.gz.md5
md5sum -c interproscan-5.27-66.0-64-bit.tar.gz.md5 （解压前，把xxx.tar.gz xxx.tar.gz.md5放到同一目录下做检查完整性）
tar -pxvzf interproscan-5.27-66.0-64-bit.tar.gz （-p参数为了保持文件的权限 -v 建议去掉，这个是解压过程显示）
（解压后进去有个data目录，后续panther数据解压放进去，配置文件默认路径，如果放其他地方，设置一下）
第三步：运行测试
./interproscan.sh -i test_proteins.fasta -f tsv
./interproscan.sh -i test_proteins.fasta -cpu 8 -f GFF3 -goterms -iprlookup -t p -T 20171127tmp
# 参数： -i 输入 -f format -goterms -iprlookup GO注释 -t 数据类型 -T 临时文件目录名称
小提示：
TSV 是Tab-separated values的缩写，即制表符分隔值。
CSV，Comma-separated values（逗号分隔值）。
#============================= 具体参数 ========================================
27/11/2017 14:41:35:049 Welcome to InterProScan-5.27-66.0
usage: java -XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts
-XX:+UseFastAccessorMethods -Xms128M -Xmx2048M -jar
interproscan-5.jar
Please give us your feedback by sending an email to
interhelp@ebi.ac.uk
-appl,--applications <ANALYSES> Optional, comma separated list
of analyses. If this option
is not set, ALL analyses will
be run.
-b,--output-file-base <OUTPUT-FILE-BASE> Optional, base output filename
(relative or absolute path).
Note that this option, the
--output-dir (-d) option and
the --outfile (-o) option are
mutually exclusive. The
appropriate file extension for
the output format(s) will be
appended automatically. By
default the input file
path/name will be used.
-cpu,--cpu <CPU> Optional, number of cores for
inteproscan.
-d,--output-dir <OUTPUT-DIR> Optional, output directory.
Note that this option, the
--outfile (-o) option and the
--output-file-base (-b) option
are mutually exclusive. The
output filename(s) are the
same as the input filename,
with the appropriate file
extension(s) for the output
format(s) appended
automatically .
-dp,--disable-precalc Optional. Disables use of the
precalculated match lookup
service. All match
calculations will be run
locally.
-dra,--disable-residue-annot Optional, excludes sites from
the XML, JSON output
-f,--formats <OUTPUT-FORMATS> Optional, case-insensitive,
comma separated list of output
formats. Supported formats are
TSV, XML, JSON, GFF3, HTML and
SVG. Default for protein
sequences are TSV, XML and
GFF3, or for nucleotide
sequences GFF3 and XML.
-goterms,--goterms Optional, switch on lookup of
corresponding Gene Ontology
annotation (IMPLIES -iprlookup
option)
-help,--help Optional, display help
information
-i,--input <INPUT-FILE-PATH> Optional, path to fasta file
that should be loaded on
Master startup. Alternatively,
in CONVERT mode, the
InterProScan 5 XML file to
convert.
-iprlookup,--iprlookup Also include lookup of
corresponding InterPro
annotation in the TSV and GFF3
output formats.
-ms,--minsize <MINIMUM-SIZE> Optional, minimum nucleotide
size of ORF to report. Will
only be considered if n is
specified as a sequence type.
Please be aware of the fact
that if you specify a too
short value it might be that
the analysis takes a very long
time!
-o,--outfile <EXPLICIT_OUTPUT_FILENAME> Optional explicit output file
name (relative or absolute
path). Note that this option,
the --output-dir (-d) option
and the --output-file-base
(-b) option are mutually
exclusive. If this option is
given, you MUST specify a
single output format using the
-f option. The output file
name will not be modified.
Note that specifying an output
file name using this option
OVERWRITES ANY EXISTING FILE.
-pa,--pathways Optional, switch on lookup of
corresponding Pathway
annotation (IMPLIES -iprlookup
option)
-t,--seqtype <SEQUENCE-TYPE> Optional, the type of the
input sequences (dna/rna (n)
or protein (p)). The default
sequence type is protein.
-T,--tempdir <TEMP-DIR> Optional, specify temporary
file directory (relative or
absolute path). The default
location is temp/.
-version,--version Optional, display version
number
-vtsv,--output-tsv-version Optional, includes a TSV
version file along with any
TSV output (when TSV output
requested)
Copyright © EMBL European Bioinformatics Institute, Hinxton, Cambridge,
UK. (http://www.ebi.ac.uk) The InterProScan software itself is provided
under the Apache License, Version 2.0
(http://www.apache.org/licenses/LICENSE-2.0.html). Third party components
(e.g. member database binaries and models) are subject to separate
licensing - please see the individual member database websites for
details.
Available analyses:
TIGRFAM (15.0) : TIGRFAMs are protein families based on Hidden Markov Models or HMMs
SFLD (3) : SFLDs are protein families based on Hidden Markov Models or HMMs
SUPERFAMILY (1.75) : SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
PANTHER (12.0) : The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
Gene3D (4.1.0) : Structural assignment for whole genes and genomes using the CATH domain structure database
Hamap (2017_10) : High-quality Automated and Manual Annotation of Microbial Proteomes
Coils (2.2.1) : Prediction of Coiled Coil Regions in Proteins
ProSiteProfiles (2017_09) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them
SMART (7.1) : SMART allows the identification and analysis of domain architectures based on Hidden Markov Models or HMMs
CDD (3.16) : Prediction of CDD domains in Proteins
PRINTS (42.0) : A fingerprint is a group of conserved motifs used to characterise a protein family
ProSitePatterns (2017_09) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them
Pfam (31.0) : A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
ProDom (2006.1) : ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.
MobiDBLite (1.0) : Prediction of disordered domains Regions in Proteins
PIRSF (3.02) : The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
Deactivated analyses:
Phobius (1.01) : Analysis Phobius is deactivated, because the resources expected at the following paths do not exist: bin/phobius/1.01/phobius.pl
SignalP_EUK (4.1) : Analysis SignalP_EUK is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp
SignalP_GRAM_POSITIVE (4.1) : Analysis SignalP_GRAM_POSITIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp
TMHMM (2.0c) : Analysis TMHMM is deactivated, because the resources expected at the following paths do not exist: bin/tmhmm/2.0c/decodeanhmm, data/tmhmm/2.0c/TMHMM2.0c.model
SignalP_GRAM_NEGATIVE (4.1) : Analysis SignalP_GRAM_NEGATIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp
