EcoliWiki - User contributions [en]

Category:GO:0015768 ! maltose transport

2010-09-25T19:34:48Z

195.42.102.25: New GO term category page

Category:GO:0004017 ! adenylate kinase activity

2010-09-25T19:30:47Z

195.42.102.25: New GO term category page

User:Rajeev

2010-09-25T19:22:30Z

195.42.102.25: Fill User: Page!

Click "edit table" in the last row to add information to the table. Click [[Help:Adding_your_information|here]] to find out how to add more information to your user page.



{| id="S4c9e4bf673346" class=" tableEdit User_info_table"

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Misra, Rajeev
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Arizona State University
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|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.176203.S4c9e4bf673346&page=176203&pagename={{FULLPAGENAMEE}}&type=1&template=User_info_table edit table] ||
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==References==
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User:Rajeev

2010-09-25T19:22:30Z

195.42.102.25: New User: Page!

User:Avijitbio

2010-09-25T19:04:28Z

195.42.102.25: Fill User: Page!

Click "edit table" in the last row to add information to the table. Click [[Help:Adding_your_information|here]] to find out how to add more information to your user page.



{| id="P4c9e47bcb69e2" class=" tableEdit User_info_table"

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pramanik, avijit
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|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.176202.P4c9e47bcb69e2&page=176202&pagename={{FULLPAGENAMEE}}&type=1&template=User_info_table edit table] ||
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==References==
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<references/>

User:Avijitbio

2010-09-25T19:04:28Z

195.42.102.25: New User: Page!

User:Bfluisi

2010-09-25T19:03:53Z

195.42.102.25: Fill User: Page!

Click "edit table" in the last row to add information to the table. Click [[Help:Adding_your_information|here]] to find out how to add more information to your user page.



{| id="G4c9e4798e92d2" class=" tableEdit User_info_table"

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!align=left |Name (Last, First)
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Luisi, Ben
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Univ. of Cambridge
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|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.176201.G4c9e4798e92d2&page=176201&pagename={{FULLPAGENAMEE}}&type=1&template=User_info_table edit table] ||
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==References==
{{RefHelp}}
<references/>

User:Bfluisi

2010-09-25T19:03:52Z

195.42.102.25: New User: Page!

User:Paul Stenmark

2010-09-25T19:03:39Z

195.42.102.25: Fill User: Page!

Click "edit table" in the last row to add information to the table. Click [[Help:Adding_your_information|here]] to find out how to add more information to your user page.



{| id="D4c9e478ad9005" class=" tableEdit User_info_table"

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!align=left |Name (Last, First)
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Stenmark, Paul
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|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.176200.D4c9e478ad9005&page=176200&pagename={{FULLPAGENAMEE}}&type=1&template=User_info_table edit table] ||
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==References==
{{RefHelp}}
<references/>

User:Paul Stenmark

2010-09-25T19:03:38Z

195.42.102.25: New User: Page!

PMID:11932250

2010-07-13T23:30:30Z

195.42.102.25: Fill PMID: Page!

{{RightTOC}}
<protect>
 '''Kent, WJ''' (2002) BLAT--the BLAST-like alignment tool.''Genome Res.'' '''12''':656-64

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || <protect>Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. It uses the index to find regions in the genome likely to be homologous to the query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible. This paper describes how BLAT was optimized. Effects on speed and sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index matches. BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11932250 PubMed]
Online version:[http://dx.doi.org/10.1101/gr.229202. Article published online before March 2002 10.1101/gr.229202. Article published online before March 2002]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Q4c3cf71627923" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.172439.Q4c3cf71627923&page=172439&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:11932250

2010-07-13T23:30:30Z

195.42.102.25: New PMID: Page!

PMID:16710451

2010-07-13T23:30:12Z

195.42.102.25: Fill PMID: Page!

{{RightTOC}}
<protect>
 '''Starmer, J, Stomp, A, Vouk, M and Bitzer, D''' (2006) Predicting Shine-Dalgarno sequence locations exposes genome annotation errors.''PLoS Comput. Biol.'' '''2''':e57

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || <protect>In prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis. The location of SD sequences relative to start codons and the stability of the hybridization between the mRNA and the rRNA correlate with the rate of synthesis. Thus, accurate characterization of SD sequences enhances our understanding of how an organism's transcriptome relates to its cellular proteome. We implemented the Individual Nearest Neighbor Hydrogen Bond model for oligo-oligo hybridization and created a new metric, relative spacing (RS), to identify both the location and the hybridization potential of SD sequences by simulating the binding between mRNAs and single-stranded 16S rRNA 3' tails. In 18 prokaryote genomes, we identified 2,420 genes out of 58,550 where the strongest binding in the translation initiation region included the start codon, deviating from the expected location for the SD sequence of five to ten bases upstream. We designated these as RS+1 genes. Additional analysis uncovered an unusual bias of the start codon in that the majority of the RS+1 genes used GUG, not AUG. Furthermore, of the 624 RS+1 genes whose SD sequence was associated with a free energy release of less than -8.4 kcal/mol (strong RS+1 genes), 384 were within 12 nucleotides upstream of in-frame initiation codons. The most likely explanation for the unexpected location of the SD sequence for these 384 genes is mis-annotation of the start codon. In this way, the new RS metric provides an improved method for gene sequence annotation. The remaining strong RS+1 genes appear to have their SD sequences in an unexpected location that includes the start codon. Thus, our RS metric provides a new way to explore the role of rRNA-mRNA nucleotide hybridization in translation initiation.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16710451 PubMed]
Online version:[http://dx.doi.org/10.1371/journal.pcbi.0020057 10.1371/journal.pcbi.0020057]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="G4c3cf704afb2f" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.172438.G4c3cf704afb2f&page=172438&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:16710451

2010-07-13T23:30:12Z

195.42.102.25: New PMID: Page!

Category:GO:0006567 ! threonine catabolic process

2010-06-07T03:37:50Z

195.42.102.25: New GO term category page

Category:GO:0004794 ! L-threonine ammonia-lyase activity

2010-06-07T03:37:19Z

195.42.102.25: New GO term category page

Category:GO:0033883 ! pyridoxal phosphatase activity

2010-06-07T03:36:47Z

195.42.102.25: New GO term category page

Category:GO:0006568 ! tryptophan metabolic process

2010-06-07T03:33:16Z

195.42.102.25: New GO term category page