bioinfo_6th_20070720

  • 1,127 views
Uploaded on

 

More in: Technology
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
1,127
On Slideshare
0
From Embeds
0
Number of Embeds
0

Actions

Shares
Downloads
0
Comments
0
Likes
0

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

  • 1. • • • • •
  • 2. • • GCATGCAT A C G T T C G T
  • 3. • • • • • • • •
  • 4. • • • 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
  • 5. >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 |||||| || ||||||||||| ||||||||||||
  • 6. $ 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
  • 7. • • • • • • • • • •
  • 8. • • • • • jsmbp:~ sesejun$ sudo port -d selfupdate ( PC jsmbp:~ sesejun$ sudo port -d install ImageMagick jsmbp:~ sesejun$ sudo port -d install ghostscript
  • 9. • • • 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 ( jsmbp:~/bin sesejun$ make (
  • 10. • • • • • • • • • •
  • 11. • • $ ~/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
  • 12. 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
  • 13. • • • • • • • • • • •
  • 14. #!/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
  • 15. • • • 1. 2. 3. 4. • •