May « 2012 « 小生这厢有礼了(BioFaceBook Personal Blog)

生物資訊教學( Good sources)

生物資訊教學

生物資訊是一門整合生命科學與電腦科學的跨領域研究。此Wiki由【計算生物學】與【生物資訊演算法】之修課學生，國立中正大學生物資訊實驗室同學，與指導老師黃耀廷博士所共同編寫。生物資訊之背景知識，涵蓋部份生物、遺傳、統計、與演算法之背景知識，可分以下子課題介紹：

生命科學遺傳演化生物統計生物資訊演算法 Assembly Tool: 沒有參考基因體(Reference Genome)的物種(例如，鴿子、蓮霧)，定序完必須把破碎的序列重組出一條參考基因體。 Assembly Tools: de bruijn graph assemblers: Velvet、Euler-SR、SOAPdenovo、ABySS、CLCBio Overlap-graph assemblers: MIRA、AMOS package Scaffolder: SOAPdenovo, SSPACE, Bambus, IMAGE2. Gene Prediction Gene Ontology Annotation Alignment Tool: 已經有參考基因體的物種(例如，人類、稻米)，定序完可以直接把序列對回去(Align)參考基因體。 Short read alignment: BOWTIE、BWA、Bfast、SOAPaligner、MAQ Alignment檔案處理: SAMTools、Tabix for range query、Split Bam、挑出成對序列 Local realignment for small indels: SAMTools、GATK Long read alignment: BLAT、BLAST使用範例、wwwblast安裝設定、Lastz […]

gene prediction pipeline

augustususe EST file blat -minIdentity=92 aphis_genome_scaffold_v3.1.fa aphis-unigene.idx.fna aphis-unigene.idx.psl /home/soft/pslCDnaFilter -maxAligns=1 aphis-unigene.idx.psl aphis-unigene.idx.f.psl /home/soft/augustus.2.5/scripts/blat2hints.pl –in=aphis-unigene.idx.f.psl –out=hints.E.gff./augustusRun.pl /public/d_aphis/DNA_assembly/3.1fix/gene_predict/augustus aphis_genome_scaffold_v3.1.fa pea_aphid hints.E.gff 15./augustusRun.py -i aphis_genome_scaffold_v3.1.fa -n pea_aphid -j hints.E.gff -s 35000000 &# —– prediction on sequence number 3 (length = 1746996, name = AGO_S000003) —–geneid:./scripts/gffftablExport.pl aphis.geneid.model.gff3 aphis.geneid geneidblast2go-rw-r–r– 1 zhaoqy users 90672652 2010-10-15 gene2go-rw-r–r– 1 zhaoqy users 19294682 […]

Gene Prediction

Bacteria Gene Prediction

* GeneMark and Glimmer This provides the foundation for operon predictions and promotor predictions. One way to verify the gene prediction result is to check the presence of Shine-Dalgarno sequence in fron of each gene which is a purine-rich region with a consensus AGGAGG and is located within 20 bp upstream of […]

My PROJECT

Amoa project

A2,A3 amoa sample sequencing

(1) use geneious to deal with the sequence raw data, get 635bp DNA sequence

(2)use mafft to get the alignment results

(3)mothur deal pipline

mothur > dist.seqs(fasta=AMOA_A2A3.mafft.align.shortname.fasta, output=lt)

0 0 59 0

Output File Name: AMOA_A2A3.mafft.align.shortname.phylip.dist

It took 0 to calculate the distances for 60 sequences.

mothur > cluster(phylip=AMOA_A2A3.mafft.align.shortname.phylip.dist, […]

做蛋白分析（2，3级结构）软件参考网站 UCSF Chimera

http://www.cgl.ucsf.edu/chimera/

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, […]

tree 统计学分析Graphpad Prism

1. 序列分类和种系分析：保守序列直接在GenBank上进行BLAST比较，所有序列使用欧洲生物信息学院的ClustalW2排列，然后用RDPII9.49进行分类。序列≧98%一致性的定为同一种，用MEGA4.0进行相邻合并分析绘制种系结构图。

2. 统计学分析：使用Graphpad Prism 软件进行配对卡方检验分析。

velvet assembly based on reference

(from a user-discussion group)

Dear Velvet users,

it’s my pleasure to announce the 1.0.01 release of Velvet!

Thanks to the Columbus module, Velvet now doubles up as an assisted assembler. In other words, if you already have sequences to guide the assembly (regions, contigs, exons, anything really), you can map the reads onto these sequences […]

python 删除列表空元素或相同元素

a=[‘a’,’b’,’c’,’a’,’d’,’a’]

如何把所有的’a’删除呢？

我的笨方法： for i in a: if i == ‘a': a[a.index(i)] = ”

while ” in a: a.remove(”)

INSTALL MicrobeDB

shenzy@shenzy-ubuntu:/usr/local/lib/perl/5.10.1/MicrobeDB/scripts$ load_genome.pl -d /home/shenzy/Downloads/unpublished_genomes/Pseudomonas_aeruginosa_LESB58/ 2012/05/15 16:01:48> Working on /home/shenzy/Downloads/unpublished_genomes/Pseudomonas_aeruginosa_LESB58/ 2012/05/15 16:01:48> Parsing file: /home/shenzy/Downloads/unpublished_genomes/Pseudomonas_aeruginosa_LESB58/Pseudomonas_aeruginoas_LESB58.gbk 2012/05/15 16:01:48> Can’t find file:/home/shenzy/Downloads/unpublished_genomes/NCBI_completegenomes.txt . GenomeProject table will not contain much organism information. 2012/05/15 16:01:48> Can’t find file:/home/shenzy/Downloads/unpublished_genomes/NCBI_completegenomes.txt . GenomeProject table will be missing a few fields of information. DBD::mysql::st execute failed: Unknown column ‘distance_calculated’ in ‘field list’ at […]

Bpipe A tool for running and managing bioinformatics pipelines

Starting from a Shell Script

In this tutorial we will develop a Bpipe pipeline script for a realistic (but simplified) analysis pipeline used for variant calling on NGS data. In this pipeline the following stages are executed:

sequence alignment using bwa sorting and indexing output files using samtools PCR duplicate removal using Picard calling variants […]

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