Blasting Spacers for Our Genome

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Blasting Spacers

EXPLORATION OF THE IMPORTANT FINDINGS


CRISPR one results from CRISPR finder are shown below. I blasted all of the spacers using the nr/nt database and the results are shown below.

CrisperOne.jpg


Spacer One: TGCGTCGTCCGGTGGCCGTCAATAAATGTCGCAAGGG

No significant hits . . . lowest E-value is 5.9

Spacer Two: TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA

  Spacer2.jpg
  
 Archaeal BJ1 virus complete genome:  Good Article
 
 Spacer2222.jpg
 
 This is the protein sequence location that this match comes from in the virus:
 
 Archaealvirus.jpg
 
 Blasted this little sequence alignment section. . .  did not get any significant viral alignments except its own
 
 Did blastp to determine if hypothetical protein in archaeal BJ1 virus had hits in other viruses:
 
 Blastp4.jpg
 
 
 The rest of the hits are bacteria and are in coding protein sequences such as ABC transporter and ATP-binding protein. 


Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA

Spacer3.jpg

All of these hits are bacteria and the bacteria hits are part of coding proteins such as conserved hypothetical protein; putative membrane protein, which I did a blastp for and found no viral matches

Spacer Four: TCACCCAAGCGCAAGCAACAGCTGATCGAGGACCTG

Spacer4.jpg

Hits come from prokaryotes and is from a coding segment

Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC

Spacer5.jpg

The following hits are the only significant hits that come from a prokaryote but are n a coding segment of DNA

Spacer Six: TGCGAGTGTTGCGGGGAACCGACTCGGGTAGGCCAG

 Spacer6.jpg
 
 Aligns with something in our genome. . . NOT another spacer but a segment of DNA that flanks two genes and is non-coding. . . 

Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG

Spacer8.jpg

Hit from a prokaryote that is in its coding region

Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC

No significant hits . . . lowest E-value is 1.2

Spacer Nine: TGGTAGGCGTCGTAGGTGTTCGTGGCGAGCGTGTC

Spacer9.jpg

Hit from prokaryote that is in its coding region

Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA

No significant hits . . . lowest E-value is 1.4

Spacer Eleven: GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC

 Spacer11.jpg
 
 Hits from gene segment in prokaryote or promoter sequence because flanking two genes

Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC

No significant hits . . . lowest E-value is 1.5

Spacer Thirteen:CCGATCACGCCCTGCCGATACTGGTAGTTCGCGATA

Spacer132.jpg

Hit from prokaryote in gene segment

Spacer Fourteen: TCGTCGGCCGGCTCGTCGGCCGACGTGGACTTGC

 Spacer142.jpg
 
 first hit from prokaryote gene region
 
 2nd hit: from virus 
 
 Spacer14more.jpg
 this virus when you blast it. . . it infects pathogens, bacteria and plant. . .maybe archaea too????

Spacer Fifteen: AGTAGGTCTAATGTCTCTCTGTCGTCTATCAGCCCCG

No significant hits . . . lowest E-value is 23

Spacer Sixteen: GCTCTCCGGTGTCACAGGTCAGGTCACGGTCTCCGC

No significant hits . . . lowest E-value is 5.6

Spacer Seventeen: ACGGACAAGTCATCCACCCGCCAGTATCTCCCGGT

Spacer17.jpg

Bad hit from prokaryote coding sequence

Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC

No significant hits . . . lowest E-value is 1.5

Spacer Nineteen: CAGATGTGGGGTCTGTGGCCACAGTCTAACATCTCT

No significant hits . . . lowest E-value is 1.4

Spacer Twenty: CCTGATAACGGACTCTTGTAGGTCCGTTAGGTCGT

No significant hits . . . lowest E-value is 5.2

Spacer Twenty-One: AAAAATGAGTGACGTAGACATTCGGCAAAATGCCGG

No significant hits . . . lowest E-value is 1.4

Spacer Twenty-Two: CAGCAGCGAAACGAGCCGTCCGTCCTTTTGAGACA

Spacer22.jpg

Hit from prokaryote in gene segment

Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG

Spacer23.jpg

Bad -values= throw out

Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG

Spacer24.jpg

Hit from prokaryote in gene segment

Spacer Twenty-Five: ACCGTTGCCGCCGATCGGCAGCGAGCCGGTGATGTGT

 Spacer252.jpg
 
 Hits from prokaryotes in flanking sequence or in gene sequence. . . check to see if this is in spacer!!
 
 Spacer26more.jpg

Spacer Twenty-Six: TCAAAGCGAGCCTCGAACGCGACGACGAAGATATG

Spacer262.jpg

Hits from prokaryotes in gene segment

Spacer Twenty-Seven: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG

No significant hits . . . lowest E-value is 1.4

Spacer Twenty-Eight: GACTGGCGTGTTGCCGTTCAGGCCGGCGTTGATCCCG

Spacer28.jpg

Hits from prokaryotes in gene segment

Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT

No significant hits . . . lowest E-value is 1.3

Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA

Spacer30.jpg

Bad e-value and top hit is a bunch of gene from bacteria

Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC

Spacer31.jpg

Hit from prokaryotes in gene segment

Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC

Spacer322.jpg

Hit from prokaryotes in gene segment

Spacer Thirty-Three: GTTGTGTGAGGTATGCGATGGACACCACCGATCACG

No significant hits . . . lowest E-value is 1.4



CRISPR Two Spacers: CHANGED parameters to be 1.-1 match/mistatch to make it less intense. . . also excluded eukaryotes NOW

Crisprtwo.jpg Crispr3.jpg

Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC

Hits from prokaryote in gene segment

Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC

No significant hits . . . lowest E-value is 1.5

Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG

Crispr2spacer3.jpg

E-values not good and prokaryotes

Spacer Four: TCGACGAGATCGGCGCGAACTCGTTCGCTGATACT

Crispr2spacer4.jpg

Hits from prokaryote in gene segment

Spacer Five: TCGGGGACCGAGACGACGGGGCCGGGTGCTGTCT

 Crispr2spacer5.jpg
 
 Hit from a virus (same virus even though
 called different names):
 
 Crispr2spacer5more.jpg

Spacer Six: CCGGAGGGGCCGCTGCGTGGGTGATCTGGAGAGAAGA

Crispr2spacer6.jpg

E-values not good and from prokaryotes

Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT

No significant hits . . . lowest E-value is 5.5

Spacer Eight: ACGGAAATCCAGCCGATCACCCTCCGAGAGGAGAGG

Crispr2spacer8.jpg

Hit from prokaryote in gene segment

Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT

No significant hits . . . lowest E-value is 5.2

Spacer Ten: CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA

 Crispr2spacer10.jpg
 
 First hit from bacteria in gene segment. . .
 
 Second hit is from another archaea in a conserved hypothetical protein. . . is this a true protein. . .??
 
 Crispr2spacer10more.jpg

Spacer Eleven: GGCTTCTACGTCGGCAACCGGACCGAGGACGGCGATG

Crispr2spacer11.jpg

Hit with significant e-value is from a bacteria in a gene segment

Spacer Twelve: AAGTACGCCTCGATCATCAACGGCGTCCGGGCTGT

Crispr2spacer12.jpg

E-values no good and from a prokaryote in a gene

Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT

No significant hits . . . lowest E-value is 1.3

Spacer Fourteen: AGCCCTTGTGCAATGATCGGGAGTGCAATCCGACC

No significant hits . . . lowest E-value is 5.2

Spacer Fifteen: TCAGGCGAGTTGTCGGACGAACAGCTTGAAGCGTGT

No significant hits . . . lowest E-value is 1.4

Spacer Sixteen: TCGTCGAGCGGCAGGCCGCCGACCGCTACGGGCTG

Crispr2spacer16.jpg

Hits from prokaryotes in gene segment

Spacer Seventeen: CGACACGGTCGAAGATGCTGGCAGCTCGCGAATCGC

Crispr2spacer17.jpg

Bad e-value

Spacer Eighteen: GGATCTCGACGGCCGCGTGGCCGTGCATCTCGGGGTC

Crispr2spacer18.jpg

Hit from prokaryote in gene segment

Spacer Nineteen: AACGCTTCAACGCGCTCTATTGACCGAGCGTATCG

No significant hits . . . lowest E-value is 1.3

Spacer Twenty: AGATCTCGCGGATAAGCTGCCCCCGCCCTCCCATGAG

No significant hits . . . lowest E-value is 5.9

Spacer Twenty-One: CACTTCGAGCGGACTTTGGGCCACCCCGGAAAGTCAG

No significant hits . . . lowest E-value is 1.5

Spacer Twenty-Two: CGATACGTCCGGGACGCCCGTGACGACCACCACTGC

Crispr2spacer21.jpg

Bad e-value

Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG

No significant hits . . . lowest E-value is 1.4

Spacer Twenty-Four: GAGCATCTCTCCAATCAGCGGTCATCAACCGCGA

Crispr2spacer24.jpg

Hits from prokaryotes in gene segment

Spacer Twenty-Five: AGTATCTGTCTACGCGATACCGCACCGTCAGAGTG

No significant hits . . . lowest E-value is 1.3

Spacer Twenty-Six: TACGACCTTCCCACTGAGGGTCTTGAGCTAACGATT

No significant hits . . . lowest E-value is 5.6

Spacer Twenty-Seven: GCGACGTGCTTACCTCTGACGCCAATATTGACCTT

No significant hits . . . lowest E-value is 5.2

Spacer Twenty-Eight: TTCATCAAGAGGCACACAAGCATGGTGCGTCCAAA

No significant hits . . . lowest E-value is 5.2

Spacer Twenty-Nine: CTGGCCTACCCGAGTCGGTTCCCCGCAGCACTCGCA

 Crispr2spacer29.jpg

Spacer Thirty: ACGATCGTCACCGACACCCTCGGGGCCGGCGGCGC

Crispr2spacer30.jpg

Hits from prokaryotes in gene segment

Spacer Thirty-One: GAAACGACCGAGACGCAAAGCGAGTTCACACAACTC

No significant hits . . . lowest E-value is 5.6

Spacer Thirty-Two: TTAGATGATCAGGTAGCCTGCTACCAGTGCAGCTGC

Crispr2spacer32.jpg

Poor e-values

Spacer Thirty-Three: GAGACCCAGCTTTGCCTTCCAGGTGATCAGCTCGTA

Crispr2spacer33.jpg

Hits from prokaryotes in gene segment

Spacer Thirty-Four: TCGAAGCGCTCGGTCGCGACGGAGACCAGCGACCAGCTG

 Crispr2spacer34.jpg
 
 weird because two hits from our species and these 2 hits are in a conserved protein sequence and not the spacer??????????
 
 Crispr2spacer34more.jpg

Spacer Thirty-Five: TGACGACCACACACACGAGGCCGTGCGTGTGCTTGTA

Crispr2spacer35.jpg

Hits from prokaryotes in gene segment

Spacer Thirty-Six: CCACGTCCCGGTGACACGCAGCTCGGTGAGATCGC

Crispr2spacer36.jpg

Hits from prokaryotes in gene segment

Spacer Thirty-Seven: CATGGAGTCTTCAACATTTCATGGGCTGGGCTTGGCC

No significant hits . . . lowest E-value is 5.9

Spacer Thirty-Eight: CGCAACCCGACGATCGAGGACGGGCCGTCCCTGGA

Crispr2spacer38.jpg

Bad e-values

Spacer Thirty-Nine: GCGTCGGACTGCGTCGATAGTGTTCGTGCTCATGTT

No significant hits . . . lowest E-value is 1.4

Spacer Forty: CAGACTTCTACTGGAAGGCGAAAACTGAGAAGGCA

No significant hits . . . lowest E-value is 5.2

Spacer Forty-One: TACGCTCGACGACCTCCGTCGTGCGCTCCAGAAGTCA

Crispr2spacer41.jpg

hit from prokaryote in gene segment

Spacer Forty-Two: GCGCTGCGGACGTGGTGTCAGAGGGGTTACCAGTAACT

No significant hits . . . lowest E-value is 1.6

Spacer Forty-Three: ACTCCGGGTACACTGGTGGCGATGCTCTACTCGCC

No significant hits . . . lowest E-value is 1.3

Spacer Forty-Four: ACACGTTTCTTTTTTTCAGGAGCCATCACTCACTC

No significant hits . . . lowest E-value is 1.3







Other things i want to do:

  compare our species spacers with themselves
  look to see if these blast results show hits to any other halophiles
  look at spacer length and number between our species and others??
  any known viruses that infect halophiles??
 blast the known viral genome against the nr/nt database and it comes up with matches: