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 11: Line 15:
  
 
'''Spacer Two''': TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA
 
'''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.
  
[[Image:spacer2.jpg]]
 
 
Archaeal BJ1 virus complete genome:  [http://www.biomedcentral.com/content/pdf/1471-2164-8-410.pdf Good Article]
 
 
[[Image:spacer2222.jpg]]
 
 
The rest of the hits are bacteria and are in coding protein sequences
 
  
 
Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA
 
Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA
  
 
[[Image:spacer3.jpg]]
 
[[Image: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
 
Spacer Four: TCACCCAAGCGCAAGCAACAGCTGATCGAGGACCTG
  
 
[[Image:spacer4.jpg]]
 
[[Image:spacer4.jpg]]
 +
 +
Hits come from prokaryotes and is from a coding segment
  
 
Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC
 
Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC
Line 32: Line 52:
 
[[Image:spacer5.jpg]]
 
[[Image:spacer5.jpg]]
  
Spacer Six: TGCGAGTGTTGCGGGGAACCGACTCGGGTAGGCCAG
+
The following hits are the only significant hits that come from a prokaryote but are n a coding segment of DNA
 
+
 
[[Image:spacer6.jpg]]
+
'''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. . .
  
 
Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG
 
Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG
  
 
[[Image:spacer8.jpg]]
 
[[Image:spacer8.jpg]]
 +
 +
Hit from a prokaryote that is in its coding region
  
 
Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC
 
Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC
Line 47: Line 73:
  
 
[[Image:spacer9.jpg]]
 
[[Image:spacer9.jpg]]
 +
 +
Hit from prokaryote that is in its coding region
  
 
Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA
 
Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA
Line 52: Line 80:
 
No significant hits . . . lowest E-value is 1.4
 
No significant hits . . . lowest E-value is 1.4
  
Spacer Eleven: GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC
+
'''Spacer Eleven''': GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC
 
+
 
[[Image:spacer11.jpg]]
+
  [[Image:spacer11.jpg]]
 +
 
 +
  Hits from gene segment in prokaryote or promoter sequence because flanking two genes
  
 
Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC
 
Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC
Line 64: Line 94:
 
[[Image:spacer132.jpg]]
 
[[Image:spacer132.jpg]]
  
Spacer Fourteen: TCGTCGGCCGGCTCGTCGGCCGACGTGGACTTGC
+
Hit from prokaryote in gene segment
  
[[Image:spacer142.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
Line 79: Line 119:
  
 
[[Image:spacer17.jpg]]
 
[[Image:spacer17.jpg]]
 +
 +
Bad hit from prokaryote coding sequence
  
 
Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC
 
Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC
Line 99: Line 141:
  
 
[[Image:spacer22.jpg]]
 
[[Image:spacer22.jpg]]
 +
 +
Hit from prokaryote in gene segment
  
 
Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG
 
Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG
  
 
[[Image:spacer23.jpg]]
 
[[Image:spacer23.jpg]]
 +
 +
Bad -values= throw out
  
 
Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG
 
Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG
Line 108: Line 154:
 
[[Image:spacer24.jpg]]
 
[[Image:spacer24.jpg]]
  
Spacer Twenty-Five: ACCGTTGCCGCCGATCGGCAGCGAGCCGGTGATGTGT
+
Hit from prokaryote in gene segment
  
[[Image:spacer252.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:spacer262.jpg]]
 
[[Image:spacer262.jpg]]
 +
 +
Hits from prokaryotes in gene segment
  
 
Spacer Twenty-Seven: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG
 
Spacer Twenty-Seven: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG
Line 123: Line 177:
  
 
[[Image:spacer28.jpg]]
 
[[Image:spacer28.jpg]]
 +
 +
Hits from prokaryotes in gene segment
  
 
Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT
 
Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT
Line 130: Line 186:
 
Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA
 
Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA
  
[[Image:spacer30.jpg]]
+
[[Image:spacer30.jpg]]  
 +
 
 +
Bad e-value and top hit is a bunch of gene from bacteria
  
 
Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC
 
Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC
  
 
[[Image:spacer31.jpg]]
 
[[Image:spacer31.jpg]]
 +
 +
Hit from prokaryotes in gene segment
  
 
Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC
 
Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC
Line 140: Line 200:
 
[[Image:spacer322.jpg]]
 
[[Image:spacer322.jpg]]
  
Spacer Thirty-Three:GTTGTGTGAGGTATGCGATGGACACCACCGATCACG
+
Hit from prokaryotes in gene segment
 +
 
 +
Spacer Thirty-Three: GTTGTGTGAGGTATGCGATGGACACCACCGATCACG
  
 
No significant hits . . . lowest E-value is 1.4
 
No significant hits . . . lowest E-value is 1.4
Line 152: Line 214:
 
[[Image:crispr3.jpg]]
 
[[Image:crispr3.jpg]]
  
'''Spacer One:''' TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC
+
Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC
  
LOTS of Hits!!!!
+
Hits from prokaryote in gene segment
  
 
Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC
 
Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC
Line 160: Line 222:
 
No significant hits . . . lowest E-value is 1.5
 
No significant hits . . . lowest E-value is 1.5
  
'''Spacer Three:''' GATCCGGAATATGAAGTGACGAACGATCCGGATACGG
+
Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG
  
 
[[Image:crispr2spacer3.jpg]]
 
[[Image:crispr2spacer3.jpg]]
  
'''Spacer Four''': TCGACGAGATCGGCGCGAACTCGTTCGCTGATACT
+
E-values not good and prokaryotes
 +
 
 +
Spacer Four: TCGACGAGATCGGCGCGAACTCGTTCGCTGATACT
  
 
[[Image:crispr2spacer4.jpg]]
 
[[Image:crispr2spacer4.jpg]]
 +
 +
Hits from prokaryote in gene segment
  
 
'''Spacer Five''': TCGGGGACCGAGACGACGGGGCCGGGTGCTGTCT
 
'''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]]
  
[[Image:crispr2spacer5.jpg]]
+
Spacer Six: CCGGAGGGGCCGCTGCGTGGGTGATCTGGAGAGAAGA
  
'''Spacer Six''': CCGGAGGGGCCGCTGCGTGGGTGATCTGGAGAGAAGA
+
[[Image:crispr2spacer6.jpg]]
  
[[Image:crispr2spacer6.jpg]]
+
E-values not good and from prokaryotes
  
 
Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT
 
Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT
Line 180: Line 253:
 
No significant hits . . . lowest E-value is 5.5
 
No significant hits . . . lowest E-value is 5.5
  
'''Spacer Eight:''' ACGGAAATCCAGCCGATCACCCTCCGAGAGGAGAGG
+
Spacer Eight: ACGGAAATCCAGCCGATCACCCTCCGAGAGGAGAGG
  
 
[[Image:crispr2spacer8.jpg]]
 
[[Image:crispr2spacer8.jpg]]
 +
 +
Hit from prokaryote in gene segment
  
 
Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT
 
Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT
Line 189: Line 264:
  
 
'''Spacer Ten''': CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA
 
'''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]]
  
[[Image:crispr2spacer10.jpg]]
+
Spacer Eleven: GGCTTCTACGTCGGCAACCGGACCGAGGACGGCGATG
  
'''Spacer Eleven''': GGCTTCTACGTCGGCAACCGGACCGAGGACGGCGATG
+
[[Image:crispr2spacer11.jpg]]
  
[[Image:crispr2spacer11.jpg]]
+
Hit with significant e-value is from a bacteria in a gene segment
  
'''Spacer Twelve''': AAGTACGCCTCGATCATCAACGGCGTCCGGGCTGT
+
Spacer Twelve: AAGTACGCCTCGATCATCAACGGCGTCCGGGCTGT
  
 
[[Image:crispr2spacer12.jpg]]
 
[[Image:crispr2spacer12.jpg]]
 +
 +
E-values no good and from a prokaryote in a gene
  
 
Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT
 
Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT
Line 212: Line 297:
 
No significant hits . . . lowest E-value is 1.4
 
No significant hits . . . lowest E-value is 1.4
  
'''Spacer Sixteen''': TCGTCGAGCGGCAGGCCGCCGACCGCTACGGGCTG
+
Spacer Sixteen: TCGTCGAGCGGCAGGCCGCCGACCGCTACGGGCTG
  
 
[[Image:crispr2spacer16.jpg]]
 
[[Image:crispr2spacer16.jpg]]
  
'''Spacer Seventeen:''' CGACACGGTCGAAGATGCTGGCAGCTCGCGAATCGC
+
Hits from prokaryotes in gene segment
 +
 
 +
Spacer Seventeen: CGACACGGTCGAAGATGCTGGCAGCTCGCGAATCGC
  
 
[[Image:crispr2spacer17.jpg]]
 
[[Image:crispr2spacer17.jpg]]
  
'''Spacer Eighteen:''' GGATCTCGACGGCCGCGTGGCCGTGCATCTCGGGGTC
+
Bad e-value
 +
 
 +
Spacer Eighteen: GGATCTCGACGGCCGCGTGGCCGTGCATCTCGGGGTC
  
 
[[Image:crispr2spacer18.jpg]]
 
[[Image:crispr2spacer18.jpg]]
 +
 +
Hit from prokaryote in gene segment
  
 
Spacer Nineteen: AACGCTTCAACGCGCTCTATTGACCGAGCGTATCG
 
Spacer Nineteen: AACGCTTCAACGCGCTCTATTGACCGAGCGTATCG
Line 236: Line 327:
 
No significant hits . . . lowest E-value is 1.5
 
No significant hits . . . lowest E-value is 1.5
  
'''Spacer Twenty-Two''': CGATACGTCCGGGACGCCCGTGACGACCACCACTGC
+
Spacer Twenty-Two: CGATACGTCCGGGACGCCCGTGACGACCACCACTGC
  
 
[[Image:crispr2spacer21.jpg]]
 
[[Image:crispr2spacer21.jpg]]
 +
 +
Bad e-value
  
 
Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG
 
Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG
Line 244: Line 337:
 
No significant hits . . . lowest E-value is 1.4
 
No significant hits . . . lowest E-value is 1.4
  
'''Spacer Twenty-Four''': GAGCATCTCTCCAATCAGCGGTCATCAACCGCGA
+
Spacer Twenty-Four: GAGCATCTCTCCAATCAGCGGTCATCAACCGCGA
  
 
[[Image:crispr2spacer24.jpg]]
 
[[Image:crispr2spacer24.jpg]]
 +
 +
Hits from prokaryotes in gene segment
  
 
Spacer Twenty-Five: AGTATCTGTCTACGCGATACCGCACCGTCAGAGTG
 
Spacer Twenty-Five: AGTATCTGTCTACGCGATACCGCACCGTCAGAGTG
Line 265: Line 360:
  
 
'''Spacer Twenty-Nine:''' CTGGCCTACCCGAGTCGGTTCCCCGCAGCACTCGCA
 
'''Spacer Twenty-Nine:''' CTGGCCTACCCGAGTCGGTTCCCCGCAGCACTCGCA
 +
 
 +
  [[Image:crispr2spacer29.jpg]]
  
[[Image:crispr2spacer29.jpg]]
+
Spacer Thirty: ACGATCGTCACCGACACCCTCGGGGCCGGCGGCGC
  
'''Spacer Thirty''': ACGATCGTCACCGACACCCTCGGGGCCGGCGGCGC
+
[[Image:crispr2spacer30.jpg]]
  
[[Image:crispr2spacer30.jpg]]
+
Hits from prokaryotes in gene segment
  
 
Spacer Thirty-One: GAAACGACCGAGACGCAAAGCGAGTTCACACAACTC
 
Spacer Thirty-One: GAAACGACCGAGACGCAAAGCGAGTTCACACAACTC
Line 276: Line 373:
 
No significant hits . . . lowest E-value is 5.6
 
No significant hits . . . lowest E-value is 5.6
  
'''Spacer Thirty-Two:''' TTAGATGATCAGGTAGCCTGCTACCAGTGCAGCTGC
+
Spacer Thirty-Two: TTAGATGATCAGGTAGCCTGCTACCAGTGCAGCTGC
  
 
[[Image:crispr2spacer32.jpg]]
 
[[Image:crispr2spacer32.jpg]]
  
'''Spacer Thirty-Three:''' GAGACCCAGCTTTGCCTTCCAGGTGATCAGCTCGTA
+
Poor e-values
 +
 
 +
Spacer Thirty-Three: GAGACCCAGCTTTGCCTTCCAGGTGATCAGCTCGTA
  
 
[[Image:crispr2spacer33.jpg]]
 
[[Image:crispr2spacer33.jpg]]
 +
 +
Hits from prokaryotes in gene segment
  
 
'''Spacer Thirty-Four:''' TCGAAGCGCTCGGTCGCGACGGAGACCAGCGACCAGCTG
 
'''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]]
  
[[Image:crispr2spacer34.jpg]]
+
Spacer Thirty-Five: TGACGACCACACACACGAGGCCGTGCGTGTGCTTGTA
  
'''Spacer Thirty-Five:''' TGACGACCACACACACGAGGCCGTGCGTGTGCTTGTA
+
[[Image:crispr2spacer35.jpg]]
  
[[Image:crispr2spacer35.jpg]]
+
Hits from prokaryotes in gene segment
  
'''Spacer Thirty-Six:''' CCACGTCCCGGTGACACGCAGCTCGGTGAGATCGC
+
Spacer Thirty-Six: CCACGTCCCGGTGACACGCAGCTCGGTGAGATCGC
  
 
[[Image:crispr2spacer36.jpg]]
 
[[Image:crispr2spacer36.jpg]]
 +
 +
Hits from prokaryotes in gene segment
  
 
Spacer Thirty-Seven: CATGGAGTCTTCAACATTTCATGGGCTGGGCTTGGCC
 
Spacer Thirty-Seven: CATGGAGTCTTCAACATTTCATGGGCTGGGCTTGGCC
Line 300: Line 409:
 
No significant hits . . . lowest E-value is 5.9
 
No significant hits . . . lowest E-value is 5.9
  
'''Spacer Thirty-Eight:''' CGCAACCCGACGATCGAGGACGGGCCGTCCCTGGA
+
Spacer Thirty-Eight: CGCAACCCGACGATCGAGGACGGGCCGTCCCTGGA
  
 
[[Image:crispr2spacer38.jpg]]
 
[[Image:crispr2spacer38.jpg]]
 +
 +
Bad e-values
  
 
Spacer Thirty-Nine: GCGTCGGACTGCGTCGATAGTGTTCGTGCTCATGTT
 
Spacer Thirty-Nine: GCGTCGGACTGCGTCGATAGTGTTCGTGCTCATGTT
Line 312: Line 423:
 
No significant hits . . . lowest E-value is 5.2
 
No significant hits . . . lowest E-value is 5.2
  
'''Spacer Forty-One:''' TACGCTCGACGACCTCCGTCGTGCGCTCCAGAAGTCA
+
Spacer Forty-One: TACGCTCGACGACCTCCGTCGTGCGCTCCAGAAGTCA
  
 
[[Image:crispr2spacer41.jpg]]
 
[[Image:crispr2spacer41.jpg]]
 +
 +
hit from prokaryote in gene segment
  
 
Spacer Forty-Two: GCGCTGCGGACGTGGTGTCAGAGGGGTTACCAGTAACT
 
Spacer Forty-Two: GCGCTGCGGACGTGGTGTCAGAGGGGTTACCAGTAACT
Line 327: Line 440:
  
 
No significant hits . . . lowest E-value is 1.3
 
No significant hits . . . lowest E-value is 1.3
 
 
  
  
Line 347: Line 458:
 
   look at spacer length and number between our species and others??
 
   look at spacer length and number between our species and others??
 
   any known viruses that infect halophiles??
 
   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: