Assembly

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Revision as of 09:07, 29 July 2011 (view source) Gnusnah (Talk | contribs) ← Older edit		Latest revision as of 09:09, 29 July 2011 (view source) Gnusnah (Talk | contribs) (Replaced content with "{{:Genome Sequencing}}")
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-	=Softwares=	+	{{:Genome Sequencing}}
-	{| class="wikitable" style="text-align:center" border="1"	+
-	|+	+
-	|-	+
-	|Software || Version || Input || Output || Location(machine/folder)	+
-	|-	+
-	|[[Newbler]] || 2.3(091027_1459) || || || panflam,panpyro	+
-	|-	+
-	|Phrap || 0.990329([[Phrap0.990329_patch]]) || ||  || panflam	+
-	|-	+
-	|Phrap || 1.090518 || ||  || panflam	+
-	|-	+
-	|Consed || 090206 || ||  || panflam	+
-	|-	+
-	|CABOG(celera) || 6.1 || sanger, 454(.sff), illumina(fastq), fastq || [[CABOG_output]] || panflam,panpyro	+
-	|-	+
-	|maq || 0.7.1 || ref:fasta, read:illumina, long read(not good) ||  || panflam,panpyro	+
-	|-	+
-	|abyss [[http://seqanswers.com/wiki/ABySS]] || 1.2.0 || 454, illumina ||  || panflam	+
-	|-	+
-	|SOAPdenovo || 1.04 || illumina ||  ||  panflam	+
-	|-	+
-	|SOAPaligner ||  || illumina ||  ||  panflam	+
-	|-	+
-	|Corrector(soap package) || 1.00 || fasta,fastq || || panflam	+
-	|-	+
-	|GapCloser(soap package) || 1.10 || fasta,fastq || || panflam	+
-	|-	+
-	|MIRA || || sanger,454,illumina ||  ||	+
-	|-	+
-	|gapResolution || || newbler results || fasta,qual ||	+
-	|-	+
-	|Dupfinisher || || ace file || ||	+
-	|-	+
-	|AutoEditor || 1.20 || .contig(TIGR) || ||	+
-	|-	+
-	|[http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=rnammer rnammer] || 1.2 || fasta || gff2 || panflam	+
-	|-	+
-	|hmmer || 2.3.2(for rnammer), 3 || || || panflam.panpyro	+
-	|-	+
-	|tRNAscan-SE || 1.23|| || ||panflam,panpyro	+
-	|-	+
-	|BlastViewer || || || ||panflam	+
-	|-	+
-	|M-GCAT || || || ||panflam,panpyro	+
-	|-	+
-	|bowtie || || illumina || ||	+
-	|-	+
-	|Velvet || || illumina || ||	+
-	|-	+
-	|MAQ || || illumina || ||	+
-	|-	+
-	|Polisher || || illumina || ||	+
-	|}	+
-		+
-	*http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment	+
-	*[http://lh3lh3.users.sourceforge.net/NGSalign.shtml (NGS toos)]	+
-	*[http://main.g2.bx.psu.edu/ galaxy web-page(NGS tools)]	+
-	*[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html fastx-toolkit]	+
-	*[http://en.wikipedia.org/wiki/List_of_alignment_visualization_software List of alignment visualization software]	+
-	*Conversion among formats [http://maq.sourceforge.net/fq_all2std.pl fa_all2std.pl]	+
-	*Inverted repeat finder [http://tandem.bu.edu/irf/irf.unix.help.html IRF help] [http://tandem.bu.edu/irf/irf305.macos.download.html download]	+

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Latest revision as of 09:09, 29 July 2011

Contents 1 Project#1 Eubacterium limosum KIST612 2 Project#2 Lactobacillus acidophilus 30SC 3 Project#3 Verrucosispora maris AB-18-032 4 Project#4 will be released soon 5 Project#5 will be released soon 6 Genome database

Project#1 Eubacterium limosum KIST612

Eubacterium limosum KIST612 is an anaerobic acetogen growing rapidly on high CO concentration.
Because this bacterium can use CO as a sole carbon/energy source making both acetate and ethanol,
it has recently drawn public attention as a model organism for bioenergy production from syn-gas
such as CO.

• Status

Project#2 Lactobacillus acidophilus 30SC

Lactobacillus acidophilus 30SC was isolated from swine intestine showing strong acid tolerance
and bile resistance. L. acidophilus 30SC produces a bacteriocin that is active over a wide range
of pH range and inhibits many gram-positive pathogenic strains. The strain can be utilized as a
potential probiotic culture incorporated in dairy foods and dietary supplements. 

• Status

Project#3 Verrucosispora maris AB-18-032

• Status

Project#4 will be released soon

Project#5 will be released soon

Genome database

Genome_database