SMART 简介----蛋白序列功能域分析

simple modular architecture research tool 

Smart官网：http://smart.embl-heidelberg.de/

SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa. For all the details, please refer to the publications on SMART.

（简单模块化架构研究工具）允许识别和注释遗传移动域以及域架构分析。在信号传导，细胞外和染色质相关蛋白中发现的超过500个结构域家族是可检测的。关于种系分布，功能类别，三级结构和功能上重要的残基，这些结构域被广泛注释。在非冗余蛋白质数据库中找到的每个域以及搜索参数和分类信息都存储在关系数据库系统中。

关于SMART的一些常见问题：

1. Can I run SMART locally?

SMART is composed of several different components. If you just want the basic searching functionality (not the web server) you can sign a license agreement, and get our set of Hidden Markov Models, alignments and thresholds. The license is free to academics, but not commercial users. For further details on the academic license, visit SMART page at EMBLEM.

If you are a commerical user, please contact biobyte solutions GmbH. They provide the commercial version of SMART, which can be completely customized based on your requirements and intergrated into your exising framework. You can also contact biobyte solutions if you need help analyzing large datasets or need general bioinformatics consulting.

Alternatively, the set of models is available via the InterPro consortium, although the InterProScan software does not implement thresholds in the same way as SMART, leading to some loss of sensitivity.

2. Is there a batch SMART / how do I search a large number of sequences?

You can use our batch access script to retreive multiple sequences from the database. It will work only for sequences or IDs which we have in the database.

For other sequences, your best bet would be to use a script to submit the sequences one by one to the SMART server. An example, ready to run script written in Perl can be downloaded here.

To make life easier for script users, show_motifs.pl has a special option (TEXTONLY=1) which will output results in an easy to parse, text-only format. You will still need to get your job id first, and use job_status.pl to fetch the results.

3. I'm looking for a phosphorylation/glycosylation/some-other-tiny-motif in my sequence. Can I use SMART for this?

The focus of SMART is to search for evolutionarily conserved protein domains rather than small sites of post-translational modification. ELM would be a good place to start looking for small motifs found in non-homologous contexts.

4. I'm curious why SMART appears to predict mostly regulatory domains and not enzymes with, say, metabolic roles?

This is because at the onset of SMART, we deliberately chose to tackle those domains that were most difficult to detect and annotate using database searching methods. Regulatory domains are, in the main, shorter and less well conserved, whereas enzymes are mostly longer and have better amino acid conservation, particularly in active site regions. If you wish to predict enzymatic domains you are advised to click-in the Pfam button, allowing searches of the Pfam HMM set.

5. Why can't I find domain X,Y or Z in my sequence?

If you send the sequence, we might be able to find out why

You can use SMART in two different modes: normal or genomic.The main difference is in the underlying protein database used. In Normal SMART, the database contains Swiss-Prot, SP-TrEMBL and stable Ensembl proteomes. In Genomic SMART, only the proteomes of completely sequenced genomes are used; Ensembl for metazoans and Swiss-Prot for the rest.

即smart分为两种模式，两者差别主要在于使用的数据库不同：

Normal SMART：Swiss-Prot, SP-TrEMBL and stable Ensembl proteomes

Genomic SMART：Ensembl for metazoans and Swiss-Prot for the rest

需要注意的是：

The protein database in Normal SMART has significant redundancy, even though identical proteins are removed. If you use SMART to explore domain architectures, or want to find exact domain counts in various genomes, consider switching to Genomic mode. The numbers in the domain annotation pages will be more accurate, and there will not be many protein fragments corresponding to the same gene in the architecture query results. Remember you are exploring a limited set of genomes, though.

优先使用Genomic SMART，用于探索结构域和寻找确定的结构域数目

官方提供perl脚本用于批量上传fasta文件，脚本下载地址：http://smart.embl-heidelberg.de/help/SMART_batch.pl

使用方式

$ perl SMART_batch.pl --inputFile sequence.fasta

默认将结果保存在文件夹SMART_results

$ perl SMART_batch.pl --help

查看脚本帮助信息

分析结果示例：