Uncharacterized Protein Family (UPF0153) (Katie Richeson) - Revision history

Karicheson: /* Genome Portal Results with Other Halophiles */

2009-09-08T01:02:48Z

‎Genome Portal Results with Other Halophiles

2009-09-08T01:01:44Z

2009-09-08T00:44:48Z

2009-09-08T00:41:24Z

2009-09-08T00:41:06Z

New page

= Uncharacterized Protein Family [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644030411 (644030411)]=

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 == Genome Portal Results with Other Halophiles ==
-I found similar nucleotide sequences in other halophiles, but these halophiles have not been annotated as of yet so the similar nucleotide sequences did not provide any additional data.
+I found similar nucleotide sequences in other halophiles using the blast aspect in [http://genome.jgi-psf.org/ genome portal] with different halophiles. But these halophiles have not been annotated as of yet so the similar nucleotide sequences did not provide any additional data.
 == Codon Bias ==
 I would like to see if the codon bias for this gene shows any sort of relation to our species or another species but I do not know how to check this.

← Older revision		Revision as of 01:01, 8 September 2009
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	== Blastx Search==		== Blastx Search==
		+	The results of the blastx search gave many hypothetical proteins or just unknown protein functions. Although, the third hit from [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=ABA7AD9G01S&log%24=prottop&blast_rank=3&list_uids=227880107 Halogeometricum borinquense] was a predicted predicted Fe-S [http://en.wikipedia.org/wiki/Oxidoreductase oxidoreductas]e, which is an enzyme that catalyses the transfer of Iron and Sulfide ions from one molecule to another.
		+
		+	== GC Content ==
		+	The GC content for this gene is [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644030411 68%] and the GC content for our species' genome is 65%. Therefore it is unlikely that this gene is an alien gene, but does not rule out the possibility of orthologs or paralogs.
		+
		+	== Genome Portal Results with Other Halophiles ==
		+	I found similar nucleotide sequences in other halophiles, but these halophiles have not been annotated as of yet so the similar nucleotide sequences did not provide any additional data.
		+
		+	== Codon Bias ==
		+	I would like to see if the codon bias for this gene shows any sort of relation to our species or another species but I do not know how to check this.

← Older revision		Revision as of 00:44, 8 September 2009
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	==Blastn Search==		==Blastn Search==
		+	No helpful results, all complete genomes. Shows that this nucleotide sequence is found in many halophiles such as [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=ABA3BV9W01S&log%24=nucltop&blast_rank=2&list_uids=222451341 Halorubrum lacusprofundi].
		+
		+	== Blastx Search==

← Older revision		Revision as of 00:41, 8 September 2009
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	= Uncharacterized Protein Family [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644030411 (644030411)]=		= Uncharacterized Protein Family [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644030411 (644030411)]=
		+
		+	==Blastn Search==