A remarkable new map of Britain shows how the nation was forged by successive waves of immigration from continental Europe over 10,000 years since the end of the last Ice Age.
Bioinformatics
Bioinformatics & Genomics with IBM Spectrum Scale and OpenStack
Compare Two Genomes
https://bcrc.bio.umass.edu/courses/spring2012/micbio/micbio660/content/blast
formatdb -i NC_010001.fna -p F -o T
blastall -p blastp -i testseq.faa -d database/NC_010001.faa -e .001 -m 9
http://www.businessinsider.com/how-to-make-a-genetically-edited-human-2015-3
BlastN megablast
time ../../bin/ncbi-blast-2.2.30+/bin/blastn -query ../../genomes/pan_troglodytes/panTro4.fa -db ../../genomes/human/human.db -outfmt 6 -task megablast -out hg38vspanTro4.out -num_threads 24
Killed
Novo teste
../../bin/ncbi-blast-2.2.30+/bin/blastn -query ../../genomes/pan_troglodytes/panTro4.fa -db ../../genomes/human/chr1/chr1.fa -outfmt 6 -task megablast -out hg38_chr1vspanTro4.out -num_threads 24
Muscle
Mummer
https://www.biostars.org/p/17914/
nucmer –prefix=hg38vspanTro4 ../../genomes/pan_troglodytes/panTro4.fa ../../genomes/human/hg38.fa
Bug!
http://seqanswers.com/wiki/Talk:MUMmer
Compiling from source!
DONE, running again!
../../bin/MUMmer3.23/nucmer –prefix=hg38vspanTro4 ../../genomes/pan_troglodytes/panTro4.fa ../../genomes/human/hg38.fa
LASTZ
http://www.bx.psu.edu/~rsharris/lastz/
Comparison HumanvsChimp
http://sourceforge.net/p/mummer/mailman/message/1532129/
Plot mummer results into circos
https://github.com/BioInf-Wuerzburg/wgaPipeline
https://github.com/BioInf-Wuerzburg/wgaPipeline/blob/191e5af17d9810d01c6be3ceee758ea432dbbf81/bin/wgaPipeline.pl
https://github.com/BioInf-Wuerzburg/wgaPipeline/blob/b70165ae877890ea510ae13ea76480c1186d5891/bin/DnadiffCircosParser.pl
http://schatzlab.cshl.edu/teaching/2013/2013-04-21.GenomeAccess.SequencingAndAssembly.pdf
nucmer –maxmatch CO92.fasta KIM.fasta
Align only chr1 of both animals
split fasta by sequence
awk ‘/^>chr/ {OUT=substr($0,2) “.fa”;print ” “>OUT}; OUT{print >OUT}’ your_input
Trying with LASTZ
https://www.biostars.org/p/17835/
https://www.biostars.org/p/3511/#3513
Small Experiment Chromossome 21 Humano e Chimp