TRNA Genes Check List 2009 - Revision history

Clcarcelen: /* 1/3 */

2009-09-03T16:40:59Z

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Clcarcelen: /* 1/3 */

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Clcarcelen: /* 1/3 */

2009-09-03T01:14:00Z

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Clcarcelen: /* 1/3 */

2009-09-01T16:41:13Z

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Clcarcelen: /* 1/3 */

2009-09-01T16:07:53Z

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Clcarcelen: /* 1/3 */

2009-09-01T04:55:05Z

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Clcarcelen: /* 1/3 */

2009-09-01T04:27:08Z

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Clcarcelen: /* 1/3 */

2009-09-01T04:25:44Z

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Olhoshing: /* Strand Alignment */

2009-09-01T04:18:36Z

‎Strand Alignment

← Older revision		Revision as of 16:40, 3 September 2009
Line 142:		Line 142:

	'''tRNA 644029847: 84398..84473(+) (76bp): tRNA-Met'''		'''tRNA 644029847: 84398..84473(+) (76bp): tRNA-Met'''
−	~~Blastn results show no promising matches~~	+	Haloarcula marismortui LOCUS AY596297
		+	S = 120 bits (132)
		+	E-value = 3.0e-38
		+	Query Coverage = 100%
		+	Identities = 73/76 (96%)
		+	Gaps = 1/76 (1%)
		+	Strand = Plus/Minus

← Older revision		Revision as of 02:02, 3 September 2009
Line 420:		Line 420:

	'''tRNA 644030693: 910533..910605(-) (73bp): tRNA-Gln'''		'''tRNA 644030693: 910533..910605(-) (73bp): tRNA-Gln'''
−	Blastn results ~~show no promising matches~~	+	Blastn results using the nr/nt database showed the following match:
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=45&list_uids=174711 Halobacterium volcanii Glu-tRNA-2]
		+	S = 55.4 bits (60)
		+	E-value = 2e-05
		+	Query Coverage = 75%
		+	Identities = 47/57 (82%)
		+	Gaps = 2/57 (3%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=50&list_uids=43444 Halobacterium cutirubrum transfer RNA-Gln (CUG)]
		+	S = 51.8 bits (56)
		+	E-value = 3e-04
		+	Query Coverage = 100%
		+	Identities = 55/73 (75%)
		+	Gaps = 0/73 (0%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=58&list_uids=174734 Halobacterium volcanii Gln-tRNA]
		+	S = 46.4 bits (50)
		+	E-value = 0.013
		+	Query Coverage = 100%
		+	Identities = 54/73 (73%)
		+	Gaps = 0/73 (0%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=63&list_uids=174709 Halobacterium volcanii Asp-tRNA]
		+	S = 42.8 bits (46)
		+	E-value = 0.16
		+	Query Coverage = 76%
		+	Identities = 43/56 (76%)
		+	Gaps = 0/56 (0%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=73&list_uids=174733 Halobacterium volcanii Pro-tRNA-3]
		+	S = 41.0 bits (44)
		+	E-value = 0.54
		+	Query Coverage = 47%
		+	Identities = 30/35 (85%)
		+	Gaps = 0/35 (0%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=81&list_uids=110835876 Giardia intestinalis tRNA-Gln (CTG) gene, strain ATCC 50803]
		+	S = 39.2 bits (42)
		+	E-value = 1.9
		+	Query Coverage = 73%
		+	Identities = 41/54 (75%)
		+	Gaps = 0/54 (0%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=86&list_uids=149812 Methanothermus fervidus Pro-, Thr-, Asp-, and Lys-tRNA gene]
		+	S = 39.2 bits (42)
		+	E-value = 1.9
		+	Query Coverage = 76%
		+	Identities = 43/56 (76%)
		+	Gaps = 1/56 (1%)
		+	Strand=Plus/Plus

@@ Line 62: / Line 62: @@
 '''tRNA 644029772: 22327..22400(-) (74bp): tRNA-Phe'''
-    Blastn results show no promising matches
+ Blastn results using the nr/nt database showed the following match:
@@ Line 76: / Line 83: @@
 '''tRNA 644029846: 84056..84128(+) (73bp): tRNA-Asn'''
-    Blastn results show no promising matches
+ Blastn results using the nr/nt database showed the following match:
 '''tRNA 644029847: 84398..84473(+) (76bp): tRNA-Met'''
      Blastn results show no promising matches
@@ Line 140: / Line 203: @@
 '''tRNA 644029994: 205883..205955(-) (73bp): tRNA-Val'''
-    Blastn results show no promising matches
+ Blastn results using the nr/nt database showed the following match:
 '''tRNA 644030243: 450911..450984(+) (74bp): tRNA-Tyr'''
-    Blastn results show no promising matches
+ Blastn results using the nr/nt database showed the following match:

@@ Line 156: / Line 156: @@
 '''tRNA 644030749: 969300..969374(+) (75bp): tRNA-Met'''
-    Blastn results show no promising matches
+ Blastn results using the nr/nt database showed the following match:
 '''tRNA 644030936: 1154730..1154803(-) (74bp): tRNA-Met'''
    [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UGVEB5H016&log%24=nucltop&blast_rank=26&list_uids=11363 Chlorella ellipsoida plastid trnR(ACG) gene for tRNA-ARG(ACG)]
      S = 44.6 bits (48)

@@ Line 160: / Line 160: @@
 '''tRNA 644030936: 1154730..1154803(-) (74bp): tRNA-Met'''
-     Blastn results show no promising matches
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UGVEB5H016&log%24=nucltop&blast_rank=26&list_uids=11363 Chlorella ellipsoida plastid trnR(ACG) gene for tRNA-ARG(ACG)]
 === 2/3 ===

← Older revision		Revision as of 04:55, 1 September 2009
Line 66:		Line 66:

	'''tRNA 644029840: 78836..78908(-) (73bp): tRNA-Arg'''		'''tRNA 644029840: 78836..78908(-) (73bp): tRNA-Arg'''
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T0CJ19301S&log%24=nucltop&blast_rank=4&list_uids=43442 Halobacterium cutirubrum transfer RNA-Arg (GCG)]
		+	S = 113 bits (61)
		+	E-value = 7e-23
		+	Query Coverage = 100%
		+	Identities = 69/73 (94%)
		+	Gaps = 0/73 (0%)
		+	Strand=Plus/Plus
		+
		+
		+	'''tRNA 644029846: 84056..84128(+) (73bp): tRNA-Asn'''
		+	Blastn results show no promising matches
		+
		+
		+	'''tRNA 644029847: 84398..84473(+) (76bp): tRNA-Met'''
		+	Blastn results show no promising matches
		+
		+
		+	'''tRNA 644029864: 95971..96043(+) (73bp): tRNA-Lys'''
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T0Y7F1W014&log%24=nucltop&blast_rank=2&list_uids=174721 Halobacterium volcanii Lys-tRNA-2]
		+	S = 108 bits (58)
		+	E-value = 3e-21
		+	Query Coverage = 100%
		+	Identities = 69/74 (93%)
		+	Gaps = 1/74 (1%)
		+	Strand=Plus/Plus
		+
		+
		+	'''tRNA 644029894: 125395..125467(-) (73bp): tRNA-Asp'''
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T15FMVM016&log%24=nucltop&blast_rank=8&list_uids=174709 Halobacterium volcanii Asp-tRNA]
		+	S = 113 bits (61)
		+	E-value = 7e-23
		+	Query Coverage = 100%
		+	Identities = 70/74 (94%)
		+	Gaps = 2/74 (2%)
		+	Strand=Plus/Plus
		+
		+
		+	'''tRNA 644029895: 125511..125583(-) (73bp): tRNA-Asp'''
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T1G3XW0016&log%24=nucltop&blast_rank=8&list_uids=174709 Halobacterium volcanii Asp-tRNA]
		+	S = 113 bits (61)
		+	E-value = 7e-23
		+	Query Coverage = 100%
		+	Identities = 70/74 (94%)
		+	Gaps = 2/74 (2%)
		+	Strand=Plus/Plus
		+
		+
		+	'''tRNA 644029917: 152036..152107(+) (72bp): tRNA-Ala'''
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T1T00SS012&log%24=nucltop&blast_rank=6&list_uids=174706 Halobacterium volcanii Ala-tRNA-2]
		+	S = 117 bits (63)
		+	E-value = 5e-24
		+	Query Coverage = 100%
		+	Identities = 69/72 (95%)
		+	Gaps = 0/72 (0%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T1T00SS012&log%24=nucltop&blast_rank=11&list_uids=174704 H. cutirubrum Ala-tRNA]
		+	Score = 111 bits (60)
		+	E-value = 2e-22
		+	Query Coverage = 100%
		+	Identities = 68/72 (94%)
		+	Gaps = 0/72 (0%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T1T00SS012&log%24=nucltop&blast_rank=13&list_uids=43458 Halobacterium cutirubrum transfer RNA-Ala (CGC)]
		+	Score = 106 bits (57)
		+	E-value = 1e-20
		+	Query Coverage = 100%
		+	Identities = 67/72 (93%)
		+	Gaps = 0/72 (0%)
		+	Strand=Plus/Plus
		+
		+
		+	'''tRNA 644029994: 205883..205955(-) (73bp): tRNA-Val'''
		+	Blastn results show no promising matches
		+
		+
		+	'''tRNA 644030243: 450911..450984(+) (74bp): tRNA-Tyr'''
		+	Blastn results show no promising matches
		+
		+
		+	'''tRNA 644030369: 587278..587363(+) (86bp): tRNA-Ser'''
		+	Blastn results show no promising matches
		+
		+
		+	'''tRNA 644030693: 910533..910605(-) (73bp): tRNA-Gln'''
		+	Blastn results show no promising matches
		+
		+
		+	'''tRNA 644030749: 969300..969374(+) (75bp): tRNA-Met'''
		+	Blastn results show no promising matches
		+
		+
		+	'''tRNA 644030936: 1154730..1154803(-) (74bp): tRNA-Met'''
		+	Blastn results show no promising matches

	=== 2/3 ===		=== 2/3 ===

← Older revision		Revision as of 04:27, 1 September 2009
Line 62:		Line 62:

	'''tRNA 644029772: 22327..22400(-) (74bp): tRNA-Phe'''		'''tRNA 644029772: 22327..22400(-) (74bp): tRNA-Phe'''
		+	Blastn results show no promising matches
		+
		+
		+	'''tRNA 644029840: 78836..78908(-) (73bp): tRNA-Arg'''

	=== 2/3 ===		=== 2/3 ===

← Older revision		Revision as of 04:25, 1 September 2009
Line 34:		Line 34:
	=== 1/3 ===		=== 1/3 ===

		+	'''tRNA 644029747: 829..904 (+) (76bp): tRNA-Cys'''
		+	Megablast results using the nr/nt database showed the following match:
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SZDXSV9016&log%24=nucltop&blast_rank=7&list_uids=148796 H.cutirubrum rRNA gene cluster, 23S rRNA, 5S rRNA and Cys-tRNA genes]
		+	S = 119 bits (64)
		+	E-value = 2e-24
		+	Query Coverage = 100%
		+	Identities = 72/76 (94%)
		+	Gaps = 0/76 (0%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SZDXSV9016&log%24=nucltop&blast_rank=8&list_uids=6468293 Haloarcula marismortui 5S rRNA gene and tRNA-Cys gene, rrnA operon]
		+	S = 86.1 bits (46)
		+	E-value = 2e-14
		+	Query Coverage = 68%
		+	Identities = 51/53 (96%)
		+	Gaps = 2/53 (3%)
		+	Strand=Plus/Plus
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SZDXSV9016&log%24=nucltop&blast_rank=9&list_uids=43554 Halobacterium halobium rRNA operon with genes for 16S rRNA, 23S rRNA, 5S rRNA and tRNA-Ala (UGC)]
		+	S = 69.4 bits (37)
		+	E-value = 2e-09
		+	Query Coverage = 52%
		+	Identities = 39/40 (97%)
		+	Gaps = 0/40 (0%)
		+	Strand=Plus/Plus
		+
		+
		+	'''tRNA 644029772: 22327..22400(-) (74bp): tRNA-Phe'''

	=== 2/3 ===		=== 2/3 ===

@@ Line 13: / Line 13: @@
 == Strand Alignment ==
-I attempted to see if the forward and reverse sequences of each tRNA would at least align with each other, which would make it very likely they are part of the same gene instead of parts of separate loci. I could not find an option to align the reverse complement in BLAST2, so I only used aPE. I had the forward and reverse sequences for Leu (Leucine):
+I attempted to see if the forward and reverse sequences of each tRNA would at least align with each other, which would make it very likely they are part of the same gene instead of parts of separate loci. I could not find an option to align the reverse complement in BLAST2, so I only used [http://www.biology.utah.edu/jorgensen/wayned/ape/ aPE (A Plasmid Editor)]. I had the forward and reverse sequences for Leu (Leucine):
 [[Image:Leu-align-FandR.png|center|650px]]
@@ Line 28: / Line 28: @@
 [[Image:tRNA-rev-align.png|center|650px]]
 == BLAST Hits ==