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GCATGCAT
A
C
G
T
T
C
G
T

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BLASTN 2.2.16 [Mar-25-2007]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search
programsquot;, Nucleic Acids Res. 25:3389-3402.
Query= ORFN:12 Multiple, Contig c912 1285-2874 reverse complement
(1590 letters)
Database: yeast.nt
17 sequences; 12,155,026 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
ref|NC_001143.1| Saccharomyces cerevisiae chromosome XI, complet... 72 4e-12
ref|NC_001133.1| Saccharomyces cerevisiae chromosome I, complete... 72 4e-12

6. >ref|NC_001143.1| Saccharomyces cerevisiae chromosome XI, complete chromosome
sequence
Length = 666445
Score = 71.9 bits (36), Expect = 4e-12
Identities = 75/88 (85%)
Strand = Plus / Plus
Query: 946 attactgttacttcctgtgagtctggtgtctgctctgaaaccgcttctcccgctattgtt 1005
||||| |||||||| ||||||||||||||||| || ||||| ||||| || ||||| |||
Sbjct: 648979 attacggttacttcttgtgagtctggtgtctgttccgaaactgcttcacctgctatcgtt 649038
Query: 1006 tccacagccacaaccaccatcaatgatg 1033
|| |||||||| | ||| |||||||||
Sbjct: 649039 tcgacagccactgctaccgtcaatgatg 649066
Score = 71.9 bits (36), Expect = 4e-12
Identities = 75/88 (85%)
Strand = Plus / Plus
Query: 1099 attactgttacttcctgtgagtctggtgtctgctctgaaaccgcttctcccgctattgtt 1158
||||| |||||||| ||||||||||||||||| || ||||| ||||| || ||||| |||
Sbjct: 648979 attacggttacttcttgtgagtctggtgtctgttccgaaactgcttcacctgctatcgtt 649038
Query: 1159 tccacagccacaaccaccatcaatgatg 1186
|| |||||||| | ||| |||||||||
Sbjct: 649039 tcgacagccactgctaccgtcaatgatg 649066
Score = 44.1 bits (22), Expect = 0.001
Identities = 31/34 (91%)
Strand = Plus / Plus
Query: 1479 atctagcaccgcctctttagaaatgtcaagctac 1512
|||||| || ||||||||||| ||||||||||||

7. $ cd ~/work/blast/bayanus/
$ curl -o 12.genome.fasta quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/
efetch.fcgi?
db=genome&id=NC_001143.1&seq_start=648879&seq_stop=649166&strand=1&rettype=fastaquot;
>gi|6322623:648879-649066 Saccharomyces cerevisiae chromosome XI, complete
chromosome sequence
CATCAATGGGATTACCACTGAATATACTACATGGTGCCCTCTTTCTGCTACGGAATTAACAACGGTAAGT
AAATTAGAGTCAGAAGAAAAAACCACCCTAATTACGGTTACTTCTTGTGAGTCTGGTGTCTGTTCCGAAA
CTGCTTCACCTGCTATCGTTTCGACAGCCACTGCTACCGTCAATGATG

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jsmbp:~ sesejun$ sudo port -d selfupdate
( PC
jsmbp:~ sesejun$ sudo port -d install ImageMagick
jsmbp:~ sesejun$ sudo port -d install ghostscript

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jsmbp:~ sesejun$ mkdir bin
jsmbp:~ sesejun$ cd bin
jsmbp:~/bin sesejun$ lftp ftp://emboss.open-bio.org/pub/EMBOSS
lftp emboss.open-bio.org:/pub/EMBOSS> mget EMBOSS-5.0.0.tar.gz
(
lftp emboss.open-bio.org:/pub/EMBOSS> quit
jsmbp:~/bin sesejun$ tar zxvf EMBOSS-5.0.0.tar.gz
(
jsmbp:~/bin sesejun$ cd EMBOSS-5.0.0
jsmbp:~/bin sesejun$ ./configure
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jsmbp:~/bin sesejun$ make
(

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$ ~/bin/EMBOSS-5.0.0/emboss/dotmatcher 12.genome.fasta 12.fasta
-graph ps -threshold 35 -goutfile 12.fasta
12.fasta.ps
$ convert 12.fasta.ps 12.fasta.png
ImageMagick
$ open 12.fasta.png
12.fasta.png

13. A T G C S W R Y K M B V H D N U
A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2 -4
T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2 -4
C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2 -4
S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1 -4
W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1 1
R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1 -4
Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1 1
K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1 1
M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1 -4
B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1 -1
V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1 -4
H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1 -1
D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1 -1
N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2
U -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5

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16. #!/bin/bash
for i in *.fasta.result;do
n=`echo $i | sed 's/..*//'`
echo $n
url=`ruby blastparse.rb $n.fasta.result`
case $url in
http*)
echo $url
curl -s -o $n.genome.fasta $url
~/bin/EMBOSS-5.0.0/emboss/dotmatcher $n.genome.fasta
$n.fasta -graph ps -threshold 35 -goutfile $n.fasta
convert $n.fasta.ps $n.fasta.png
;;
esac
done
10
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
db=genome&id=NC_001142.1&seq_start=722530&seq_stop=723085&strand
=2&rettype=fasta
Displays a thresholded dotplot of two sequences
Created 10.fasta.ps
101
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
db=genome&id=NC_001146.1&seq_start=57506&seq_stop=57900&strand=1
&rettype=fasta
Displays a thresholded dotplot of two sequences
Created 101.fasta.ps

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