genetics, computing, life

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bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Community Resource for the VIZBI conference series on computer methods for visualizing biological data, including genomes, protein sequences, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging.

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Didn't tested functionality but looks really coool ))

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Gene expression profiling of pre-eclamptic placentae by RNA sequencing

Pre-eclampsia is a common and complex pregnancy disorder that often involves impaired placental development. In order to identify altered gene expression in pre-eclamptic placenta, we sequenced placental transcriptomes of nine pre-eclamptic and nine healthy pregnant women in pools of three.

O! Will see whats inside! =)

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Art of seq synthesis

Download ART http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ 

linux64x: http://www.niehs.nih.gov/research/resources/assets/docs/artbinchocolatecherrycake031915linux64tgz.tgz 

 Download sequence of interest Example Human Potassium Channels: http://www.ncbi.nlm.nih.gov/gene/?term=potassium+channel+homo

let’s use KCNQ1

http://www.ncbi.nlm.nih.gov/gene/3784

Go to sequences http://www.ncbi.nlm.nih.gov/gene/3784#

http://www.ncbi.nlm.nih.gov/nuccore/NM_000218.2

Choose one of mRNAs

Get it in FASTA format

>gi|32479526|ref|NM_000218.2| Homo sapiens potassium voltage-gated channel, KQT-like subfamily, member 1 (KCNQ1), transcript variant 1, mRNA

GCGGCGGGGCTGGCAGCAGTGGCTGCCCGCACTGCGCCCGGGCGCTCGCCTTCGCTGCAGCTCCCGGTGC CGCCGCTCGGGCCGGCCCCCCGGCAGGCCCTCCTCGTTATGGCCGCGGCCTCCTCCCCGCCCAGGGCCGA GAGGAAGCGCTGGGGTTGGGGCCGCCTGCCAGGCGCCCGGCGGGGCAGCGCGGGCCTGGCCAAGAAGTGC CCCTTCTCGCTGGAGCTGGCGGAGGGCGGCCCGGCGGGCGGCGCGCTCTACGCGCCCATCGCGCCCGGCG

AND remove some seq in beginning

>gi|32479526|ref|NM_000218.2| Homo sapiens potassium voltage-gated channel, KQT-like subfamily, member 1 (KCNQ1), transcript variant 1, mRNA GCGGCGGGGCTGGCAGCAGTGGCTGCCCGCACTGCGCCCGGGCGCTCGCCTTCGCTGCAGCTCCCGGTGC CGCCGCTCGGG[CCGGCC]CCCCGGCAGGCCCTCCTCGTTATGGCCGCGGCCTCCTCCCCGCCCAGGGCCGA GAGGAAGCGCTGGGGTTGGGGCCGCCTGCCAGGCGCCCGGCGGGGCAGCGCGGGCCTGGCCAAGAAGTGC CCCTTCTCGCTGGAGCTGGCGGAGGGCGGCCCGGCGGGCGGCGCGCTCTACGCGCCCATCGCGCCCGGCG

Then let’s synthese reads

Normal

art_illumina -i KCNQ1_ts1.fasta -l 75 -ss HS25 -f 50 -o KCNQ1_ts

Mutated

art_illumina -i KCNQ1_ts1_del_CCGGCC.fasta -l 75 -ss HS25 -f 50 -o KCNQ1_ts1_del_CCGGCC

Now align it to hg19 and see in browser

bwa mem ~/ref/bwa/hg19.fa KCNQ1_ts1_del_CCGGCC.fq | awk -F'\t' '{if($4 != 0){print;}}' | samtools view -Shu - | samtools sort - KCNQ1_ts1_del_CCGGCC.fq.sorted

samtools index KCNQ1_ts1_del_CCGGCC.fq.sorted.bam

bwa mem ~/ref/bwa/hg19.fa KCNQ1_ts1.fq | awk -F'\t' '{if($4 != 0){print;}}' | samtools view -Shu - | samtools sort - KCNQ1_ts1.fq.sorted

samtools index KCNQ1_ts1.fq.sorted.bam

See results in IGV genome browser

[wowater]

Simple idea of representing sequence using turle graphics:

A,T - turn left

G,C - turn right

Two versions : 60 degrees and 30 degrees

Repeats look’s cool, also thing that mutations will be detectable by angle

It's part of human oxytocine gene with polyA at the end

Here is a code:

import turtle

sequence='cgctgcgctgccaggaggagaactacctgccgtcgccctgccagtccggccagaaggcgtgcgggagcgggggccgctgcgcggtcttgggcctctgctgcagcccggacggctgccacgccgaccctgcctgcgacgcggaagccaccttctcccagcgctgaaacttgatggctccgaacaccctcgaagcgcgccactcgcttcccccatagccaccccagaaatggtgaaaataaaataaagcaggtttttctcctctaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'

degree=90 distance=6 coef=1.008 turtle.screensize(1500,1500) ts = turtle.getscreen() print ts.window_height() print ts.window_width() seq = turtle.Turtle() # Create a turtle, assign to seq seq.pensize(1.5) turtle.delay(0) seq.ht() def adenine(): seq.pencolor("red") seq.left(degree) seq.forward(distance) def tymine(): seq.pencolor("blue") seq.left(degree) seq.forward(distance) def guanine(): seq.pencolor("lightgreen") seq.right(degree) seq.forward(distance) def cytosine(): seq.pencolor("black") seq.right(degree) seq.forward(distance) for nuc in sequence: if nuc == "a": adenine() elif nuc == "t": tymine() elif nuc == "g": guanine() elif nuc == "c": cytosine distance=distance*coef ts.getcanvas().postscript(file="seq.eps") turtle.exitonclick() #seq.ht()

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Mus musculus vs non-mus rodent transcriptome coverage

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Using new samtools mpileup 1.2

samtools mpileup -uf ref.fa file.bam | bcftools call -mv | vcf-annotate -f +/d=20/1=0.05/2=0.05/3=0.05/4=0.05/ > result.vcf

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Проекты секвенирования геномов:

http://www.genomicsengland.co.uk/the-100000-genomes-project/ https://esp.gs.washington.edu/drupal/ http://www.personalgenomes.org/uk http://www.genomes2people.org/babyseqproject/ http://www.genomes2people.org/g2p/ http://www.1000genomes.org/ https://genome10k.soe.ucsc.edu/ http://www.fargen.fo/en/ http://autismgenome10k.org/projectinformation.html http://www.nlgenome.nl/ Saudi human genome program http://rc.kfshrc.edu.sa/sgp/# http://www.bbc.com/news/health-25216135 BGI 1.000.000 Genomes есть только в новостях, на сайте BGI не подтверждают http://biotech.about.com/od/investinginbiotech/a/Bgi-Plans-To-Sequence-The-World.htm Leroy Hood P4 http://blog.23andme.com/health-traits/listening-to-leroy-hood/ http://p4mi.org/ https://www.systemsbiology.org/p4-medicine

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Make Hotspot file for ionReporter

I want to have file with all snps from snp138 database after exome variant calling - so my goal is to create a compatible bed file. It was easy to find description here: http://mendel.iontorrent.com/ion-docs/BED-File-Formats-and-Examples_64062608.html#BEDFileFormatsandExamples-PartialexampleofaHotSpotsBEDfile lala fa 1. Get all snp's plus reference alleles:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e ' select S.chrom, S.chromStart, S.chromEnd, S.name, concat("REF=",S.refNCBI,";OBS=;"), "." from snp138 as S limit 10;'

2. Select snps in exome target region

intersectBed -a snp138_all.bed -b AmpliSeqExome.20130612.Designed.bed > snp138_all_in_Ampliseq.bed

3. Add some heading and file is ready

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Hot on Your Trail: Privacy, Your Data, and Who Has Access to It

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beautiful visualizations of algorithms

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Haploreg ist one of my favorite tools when I need to get new hypothesis about snp associated with phenotype. It looks for snaps in LD with target snp and finds if they are in transcription factor binding sites or dnase hypersensitivity sites in different cell types

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Cool sound and new word

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ColorSpace