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

Click to access 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