生物信息学数据库及软件介绍--学

Website of BLAST http://www.ncbi.nlm.nih.gov/BLAST/ (BLAST2.0) http://www2.ebi.ac.uk/blast2/ (WU-Blast2) http://blast.wustl.edu/ (WU-Blast2)
Why use BLAST?
Database Retrieval
Sequencing Project Management
Restriction Mapping
Nucleic Acid Sequences
DNA/RNA Folding Database Retrieval
Primer Design Nucleic Acid Sequence Analysis
RNA secondary structure analysis
Rnastructure http://rna.chem.rochester.edu/register.html
RNAdraw http://www.rnadraw.com/ Mfold
http://frontend.bioinfo.rpi.edu/applications/mfold/cgibin/rna-form1.cgi
http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker
http://www.cbrc.jp/research/db/TFSEARCH.html
输入DNA 序列
http://www.fruitfly.org/seq_tools/promoter.html
Here we consider the use of Bioinformatics tools rather than their design and construction
Here we consider the access and analysis of data and information items rather than their generation, storage or annotation
DNA potentially encodes six proteins
Step 2 : Gene genome location analysis
UCSC : http://genome.ucsc.edu/
Paste DNA or protein sequence here in the FASTA format
Seeking Coding regions
Protein Sequences Translation to amino acids Pairwise Sequence Comparison Database Similarity Searching
Protein Sequence analysis
http://www.genome.jp/kegg/
Step 6 : Protein sequence analysis
氨基酸的理化性质分析
ExPASy
蛋白质的亚细胞定位
Psortb
TMHMM; HMMTop;HMMER
膜蛋白的跨膜区预测
蛋白质序列的二级结构预测
Jpred; Prediction protein
序列存取号
http://www.ncbi.nlm.nih.gov 基因定义
数据库标识符
Sequence Translation and ORF finding:


ORFfinder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html); 基因探索者； MEGA4, Generunner
输入DNA 序列
http://www.ebi.ac.uk/emboss/cpgplot/
http://utrdb.ba.itb.cnr.it/
Step 5 : Gene function and Pathway
http://genemerge.bioteam.net/
http://amigo.geneontology.org/cgi-bin/gost/gost.cgi
Tertiary Structure
Database:
生物软件网
http://www.bio-soft.net/
Step1Database Retrieval


melanogaster); Accession Number (NM_057605);
Key words (AChE AND Drosophila
Multiple Sequence Alignment
Prediction of Function
Phylogeny
Motifs and Patterns
Structure prediction
Structure analysis
Pipeline:
Database Retrieval Genome information analysis Sequence Translation and ORF Finding
RNAfold http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
Can be installed locally or run via a WWW page
Michael 百度文库uker`s Programs
Step 4: DNA sequence analysis
生物学家：We have a dream…
http://www.megasoftware.net/mega.html
Software Tools for Sequence Analysis Available by anonymous ftp
Windows, Macintosh, UNIX
Incorporated into the EMBOSS general package Commercial, but reasonable
蛋白质三维结构数据库（Protein Data Bank, PDB） http://www.pdb.org
Swiss-PdbViewer Raswin : software
PDF file
Step 7: Multiple alignment

To install Vector NTI Suite 7.0 To use Align X program Genedoc Clustal X : Window Clustal W :DOS Align X BioEdit 7.0.5 T-Coffee 5.05
同源和相似
1. 同源（homology）- 具有共同的祖先
直向同源（Orthologous ） 共生同源（paralogous ）
2.相似（similarity）
同源序列一般是相似的
相似序列不一定是同源的
一般认为，蛋白质序列间至少有 80个氨基酸左右的区 域有25%或更高的同源性；DNA序列具有 75%以上的 同源性有潜在的生物学意义。
Windows, Macintosh, UNIX
Incorporated into the EMBOSS general package
Pipeline:
How to creat & query a local BLAST
database using Bioedit
生物信息学数据库及软 件介绍
Bioinformatics
The design, construction and use of software tools to generate, store, annotate, access and analyse data and information relating to Molecular Biology





Tandem repeat analysis ; Transposons analysis; CpG island; Promoter prediction; Transcriptional element analysis; UTR analysis;
http://tandem.bu.edu/trf/trf.html
Different sequence analysis tools

Web-serve or online software;

Local software:
Window/DOS; Standard Unix/Linux tools;
Sequence Analysis – an Overview
RPS-BLAST
Pattern and profile searches
InterProScan
Secondary structure prediction:
Jpred
Prediction protein
Prediction protein
Swiss-Prot蛋白序列数据库和TrEMBL 由瑞士生物信息学研究所维护，蛋白质一级结构序列数据 http://www.expasy.org/sprot/
Choose the BLAST program Program Input
1 blastn blastp blastx tblastn DNA DNA
Database 1
protein 6 DNA
protein protein
6
protein 36 DNA
tblastx
DNA
DNA
Picture Result
蛋白质序列的三级结构预测
Swissmodel; PDB
ExPASy to access protein and DNA sequences
http://www.expasy.ch/
Secondary prediction
蛋白质的亚细胞定位
膜蛋白的跨膜区预测
HMMTOP
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

Http://www.ebi.ac.uk/clustalv
http://evolution.genetics.washington.edu/phylip/software.html
Here are some 369 of the phylogeny packages, and 53 free servers, that I know about. It is an attempt to be completely comprehensive.
BLASTN
Multiple Alignment
BLASTP
GO
DNA/RNA Folding
Phylogeny
Motifs and Patterns
KEGG
Secondary Structure
CpG island
Transposons
Tandem repeat
Promoter,Transcription
BLAST searching is fundamental to understanding the relatedness of any favorite query sequence to other known proteins or DNA sequences.
Applications include • identifying orthologs and paralogs • discovering new genes or proteins • discovering variants of genes or proteins • investigating expressed sequence tags (ESTs) • exploring protein structure and function
BLAT output includes browser and other formats
Step 3. Database Similarity Searching
BLAST ( Basic Local Alignment Search Tool) allows rapid sequence comparison of a query sequence against a database. 基本局域联配搜寻工具