Difference between revisions of "Blasting Spacers for Our Genome"

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== Blasting Spacers ==
 
== 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.
 
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.
Line 8: Line 12:
 
Spacer One: TGCGTCGTCCGGTGGCCGTCAATAAATGTCGCAAGGG
 
Spacer One: TGCGTCGTCCGGTGGCCGTCAATAAATGTCGCAAGGG
  
−
[[Image:spacerOne.jpg]]
+
No significant hits . . . lowest E-value is 5.9
  
−
Matches by chance!
+
'''Spacer Two''': TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA
 +
 
 +
  [[Image:spacer2.jpg]]
 +
 
 +
  Archaeal BJ1 virus complete genome:  [http://www.biomedcentral.com/content/pdf/1471-2164-8-410.pdf Good Article]
 +
 
 +
  [[Image:spacer2222.jpg]]
 +
 
 +
  This is the protein sequence location that this match comes from in the virus:
 +
 
 +
  [[Image: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:
 +
 
 +
  [[Image:blastp4.jpg]]
 +
 
 +
 
 +
  The rest of the hits are bacteria and are in coding protein sequences such as ABC transporter and ATP-binding protein.
  
−
Spacer Two: TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA
 
  
−
[[Image:spacerTwo.jpg]]
+
Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA
  
−
Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA
+
[[Image:spacer3.jpg]]
  
−
[[Image:spacerThree.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
 
Spacer Four: TCACCCAAGCGCAAGCAACAGCTGATCGAGGACCTG
  
−
[[Image:spacerFour.jpg]]
+
[[Image:spacer4.jpg]]
−
[[Image:spacerFourTwo.jpg]]
+
 
 +
Hits come from prokaryotes and is from a coding segment
  
 
Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC
 
Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC
  
−
[[Image:spacerFive.jpg]]
+
[[Image:spacer5.jpg]]
  
−
This image is only part of it. . .  
+
The following hits are the only significant hits that come from a prokaryote but are n a coding segment of DNA
 +
 
 +
'''Spacer Six''': TGCGAGTGTTGCGGGGAACCGACTCGGGTAGGCCAG
 +
 
 +
  [[Image:spacer6.jpg]]
 +
 
 +
  Aligns with something in our genome. . . NOT another spacer but a segment of DNA that flanks two genes and is non-coding. . .  
  
−
[[Image:spacerFiveTwo.jpg]]
+
Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG
  
 +
[[Image:spacer8.jpg]]
  
−
NOTE: lots of hits from each organism- indicates that multiple parts have been incorporated into our species' spacers. . . interesting to study what genes have been inserted
+
Hit from a prokaryote that is in its coding region
−
 
 
−
Spacer Six: TGCGAGTGTTGCGGGGAACCGACTCGGGTAGGCCAG
 
−
 
 
−
[[Image:spacerSix.jpg]]
 
−
 
 
−
No viral insertions in this spacer
 
−
 
 
−
Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG
 
−
 
 
−
[[Image:spacerSeven.jpg]]
 
  
 
Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC
 
Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC
  
−
[[Image:spacerEight.jpg]]
+
No significant hits . . . lowest E-value is 1.2
  
−
E-values not good- no significant hits!
+
Spacer Nine: TGGTAGGCGTCGTAGGTGTTCGTGGCGAGCGTGTC
  
−
Spacer Nine: TGGTAGGCGTCGTAGGTGTTCGTGGCGAGCGTGTC
+
[[Image:spacer9.jpg]]
  
−
[[Image:spacerNine.jpg]]
+
Hit from prokaryote that is in its coding region
  
 
Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA
 
Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA
  
−
No significant hits. . . lowest E-value is 1.5
+
No significant hits . . . lowest E-value is 1.4
  
−
Spacer Eleven: GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC
+
'''Spacer Eleven''': GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC
−
 
+
 
−
[[Image:spacerEleven.jpg]]
+
  [[Image:spacer11.jpg]]
 +
 
 +
  Hits from gene segment in prokaryote or promoter sequence because flanking two genes
  
 
Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC
 
Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC
  
−
No significant hits. . . lowest E-value is 1.6
+
No significant hits . . . lowest E-value is 1.5
  
 
Spacer Thirteen:CCGATCACGCCCTGCCGATACTGGTAGTTCGCGATA
 
Spacer Thirteen:CCGATCACGCCCTGCCGATACTGGTAGTTCGCGATA
  
−
[[Image:spacer13.jpg]]
+
[[Image:spacer132.jpg]]
  
−
Spacer Fourteen: TCGTCGGCCGGCTCGTCGGCCGACGTGGACTTGC
+
Hit from prokaryote in gene segment
  
−
[[Image:spacer14.jpg]]
+
'''Spacer Fourteen''': TCGTCGGCCGGCTCGTCGGCCGACGTGGACTTGC
 +
 
 +
  [[Image:spacer142.jpg]]
 +
 
 +
  first hit from prokaryote gene region
 +
 
 +
  2nd hit: from [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=FSHC5VSU01S&log%24=nuclalign&blast_rank=3&list_uids=163716581 virus]
 +
 
 +
  [[Image:spacer14more.jpg]]
 +
 
 +
  this virus when you blast it. . . it infects pathogens, bacteria and plant. . .maybe archaea too????
  
 
Spacer Fifteen: AGTAGGTCTAATGTCTCTCTGTCGTCTATCAGCCCCG
 
Spacer Fifteen: AGTAGGTCTAATGTCTCTCTGTCGTCTATCAGCCCCG
  
−
No significant hits. . . lowest E-value is 1.6
+
No significant hits . . . lowest E-value is 23
  
 
Spacer Sixteen: GCTCTCCGGTGTCACAGGTCAGGTCACGGTCTCCGC
 
Spacer Sixteen: GCTCTCCGGTGTCACAGGTCAGGTCACGGTCTCCGC
  
−
No significant hits . . . lowest E-value is 1.5
+
No significant hits . . . lowest E-value is 5.6
  
 
Spacer Seventeen: ACGGACAAGTCATCCACCCGCCAGTATCTCCCGGT
 
Spacer Seventeen: ACGGACAAGTCATCCACCCGCCAGTATCTCCCGGT
  
−
No significant hits . . . lowest E-value is 1.4
+
[[Image:spacer17.jpg]]
 +
 
 +
Bad hit from prokaryote coding sequence
  
 
Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC
 
Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC
  
−
No significant hits . . . lowest E-value is 6.4
+
No significant hits . . . lowest E-value is 1.5
  
 
Spacer Nineteen: CAGATGTGGGGTCTGTGGCCACAGTCTAACATCTCT
 
Spacer Nineteen: CAGATGTGGGGTCTGTGGCCACAGTCTAACATCTCT
  
−
[[Image:spacer19.jpg]]
+
No significant hits . . . lowest E-value is 1.4
  
 
Spacer Twenty: CCTGATAACGGACTCTTGTAGGTCCGTTAGGTCGT
 
Spacer Twenty: CCTGATAACGGACTCTTGTAGGTCCGTTAGGTCGT
  
−
No significant hits . . . lowest E-value is 22
+
No significant hits . . . lowest E-value is 5.2
  
 
Spacer Twenty-One: AAAAATGAGTGACGTAGACATTCGGCAAAATGCCGG
 
Spacer Twenty-One: AAAAATGAGTGACGTAGACATTCGGCAAAATGCCGG
  
−
No significant hits . . . lowest E-value is 6
+
No significant hits . . . lowest E-value is 1.4
  
 
Spacer Twenty-Two: CAGCAGCGAAACGAGCCGTCCGTCCTTTTGAGACA
 
Spacer Twenty-Two: CAGCAGCGAAACGAGCCGTCCGTCCTTTTGAGACA
  
−
No significant hits . . . lowest E-value is 1.2
+
[[Image:spacer22.jpg]]
 +
 
 +
Hit from prokaryote in gene segment
  
 
Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG
 
Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG
  
−
No significant hits . . . lowest E-value is 0.43
+
[[Image:spacer23.jpg]]
 +
 
 +
Bad -values= throw out
  
 
Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG
 
Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG
  
−
No significant hits . . . lowest E-value is 1.4
+
[[Image:spacer24.jpg]]
  
−
Spacer Twenty-Five: ACCGTTGCCGCCGATCGGCAGCGAGCCGGTGATGTGT
+
Hit from prokaryote in gene segment
  
−
[[Image:spacer25.jpg]]
+
'''Spacer Twenty-Five''': ACCGTTGCCGCCGATCGGCAGCGAGCCGGTGATGTGT
 +
 
 +
  [[Image:spacer252.jpg]]
 +
 
 +
  Hits from prokaryotes in flanking sequence or in gene sequence. . . check to see if this is in spacer!!
 +
 
 +
  [[Image:spacer26more.jpg]]
  
 
Spacer Twenty-Six:  TCAAAGCGAGCCTCGAACGCGACGACGAAGATATG
 
Spacer Twenty-Six:  TCAAAGCGAGCCTCGAACGCGACGACGAAGATATG
  
−
[[Image:spacer26.jpg]]
+
[[Image:spacer262.jpg]]
  
−
Spacer Twenty 27: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG
+
Hits from prokaryotes in gene segment
  
−
No significant hits . . . lowest E-value is 6.0
+
Spacer Twenty-Seven: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG
 +
 
 +
No significant hits . . . lowest E-value is 1.4
  
 
Spacer Twenty-Eight: GACTGGCGTGTTGCCGTTCAGGCCGGCGTTGATCCCG
 
Spacer Twenty-Eight: GACTGGCGTGTTGCCGTTCAGGCCGGCGTTGATCCCG
  
−
[[Image:spacer27.jpg]]
+
[[Image:spacer28.jpg]]
 +
 
 +
Hits from prokaryotes in gene segment
  
 
Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT
 
Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT
  
−
No significant hits . . . lowest E-value is 0.36
+
No significant hits . . . lowest E-value is 1.3
  
 
Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA
 
Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA
  
−
No significant hits . . . lowest E-value is 1.4
+
[[Image:spacer30.jpg]]
 +
 
 +
Bad e-value and top hit is a bunch of gene from bacteria
  
 
Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC
 
Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC
  
−
No significant hits . . . lowest E-value is 1.3
+
[[Image:spacer31.jpg]]
 +
 
 +
Hit from prokaryotes in gene segment
  
 
Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC
 
Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC
  
−
[[Image:spacer32.jpg]]
+
[[Image:spacer322.jpg]]
  
−
Spacer Thirty-Three:GTTGTGTGAGGTATGCGATGGACACCACCGATCACG
+
Hit from prokaryotes in gene segment
  
−
No significant hits . . . lowest E-value is 6
+
Spacer Thirty-Three: GTTGTGTGAGGTATGCGATGGACACCACCGATCACG
  
 +
No significant hits . . . lowest E-value is 1.4
  
  
  
−
CRISPR Two Spacers:
+
 
 +
CRISPR Two Spacers: CHANGED parameters to be 1.-1 match/mistatch to make it less intense. . . also excluded eukaryotes NOW
 +
 
 
[[Image:crisprtwo.jpg]]
 
[[Image:crisprtwo.jpg]]
 
[[Image:crispr3.jpg]]
 
[[Image: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
 +
 +
[[Image:crispr2spacer3.jpg]]
 +
 +
E-values not good and prokaryotes
 +
 +
Spacer Four: TCGACGAGATCGGCGCGAACTCGTTCGCTGATACT
 +
 +
[[Image:crispr2spacer4.jpg]]
 +
 +
Hits from prokaryote in gene segment
 +
 +
'''Spacer Five''': TCGGGGACCGAGACGACGGGGCCGGGTGCTGTCT
 +
 
 +
  [[Image:crispr2spacer5.jpg]]
 +
 
 +
  Hit from a [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=FW14AEYZ01S&log%24=nucltop&blast_rank=3&list_uids=255927524 virus] (same virus even though
 +
  called different names):
 +
 
 +
  [[Image:crispr2spacer5more.jpg]]
 +
 +
Spacer Six: CCGGAGGGGCCGCTGCGTGGGTGATCTGGAGAGAAGA
 +
 +
[[Image:crispr2spacer6.jpg]]
 +
 +
E-values not good and from prokaryotes
 +
 +
Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT
 +
 +
No significant hits . . . lowest E-value is 5.5
 +
 +
Spacer Eight: ACGGAAATCCAGCCGATCACCCTCCGAGAGGAGAGG
 +
 +
[[Image:crispr2spacer8.jpg]]
 +
 +
Hit from prokaryote in gene segment
 +
 +
Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT
 +
 +
No significant hits . . . lowest E-value is 5.2
 +
 +
'''Spacer Ten''': CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA
 +
 
 +
  [[Image:crispr2spacer10.jpg]]
 +
 
 +
  First hit from bacteria in gene segment. . .
 +
 
 +
  Second hit is from another [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=FW1UZWFK01S&log%24=nuclalign&blast_rank=3&list_uids=125860746 archaea] in a conserved hypothetical protein. . . is this a true protein. . .??
 +
 
 +
  [[Image:crispr2spacer10more.jpg]]
 +
 +
Spacer Eleven: GGCTTCTACGTCGGCAACCGGACCGAGGACGGCGATG
 +
 +
[[Image:crispr2spacer11.jpg]]
 +
 +
Hit with significant e-value is from a bacteria in a gene segment
 +
 +
Spacer Twelve: AAGTACGCCTCGATCATCAACGGCGTCCGGGCTGT
 +
 +
[[Image: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
 +
 +
[[Image:crispr2spacer16.jpg]]
 +
 +
Hits from prokaryotes in gene segment
 +
 +
Spacer Seventeen: CGACACGGTCGAAGATGCTGGCAGCTCGCGAATCGC
 +
 +
[[Image:crispr2spacer17.jpg]]
 +
 +
Bad e-value
 +
 +
Spacer Eighteen: GGATCTCGACGGCCGCGTGGCCGTGCATCTCGGGGTC
 +
 +
[[Image: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
 +
 +
[[Image:crispr2spacer21.jpg]]
 +
 +
Bad e-value
 +
 +
Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG
 +
 +
No significant hits . . . lowest E-value is 1.4
 +
 +
Spacer Twenty-Four: GAGCATCTCTCCAATCAGCGGTCATCAACCGCGA
 +
 +
[[Image: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
 +
 
 +
  [[Image:crispr2spacer29.jpg]]
 +
 +
Spacer Thirty: ACGATCGTCACCGACACCCTCGGGGCCGGCGGCGC
 +
 +
[[Image: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
 +
 +
[[Image:crispr2spacer32.jpg]]
 +
 +
Poor e-values
 +
 +
Spacer Thirty-Three: GAGACCCAGCTTTGCCTTCCAGGTGATCAGCTCGTA
 +
 +
[[Image:crispr2spacer33.jpg]]
 +
 +
Hits from prokaryotes in gene segment
 +
 +
'''Spacer Thirty-Four:''' TCGAAGCGCTCGGTCGCGACGGAGACCAGCGACCAGCTG
 +
 
 +
  [[Image:crispr2spacer34.jpg]]
 +
 
 +
  weird because two hits from our species and these 2 hits are in a conserved protein sequence and not the spacer??????????
 +
 
 +
  [[Image:crispr2spacer34more.jpg]]
 +
 +
Spacer Thirty-Five: TGACGACCACACACACGAGGCCGTGCGTGTGCTTGTA
 +
 +
[[Image:crispr2spacer35.jpg]]
 +
 +
Hits from prokaryotes in gene segment
 +
 +
Spacer Thirty-Six: CCACGTCCCGGTGACACGCAGCTCGGTGAGATCGC
 +
 +
[[Image: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
 +
 +
[[Image: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
 +
 +
[[Image: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:

Latest revision as of 01:56, 14 November 2009

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:
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