Annotate-a-genome - Revision history

imported>Weigang: /* Claim your assigned genome */

2014-05-23T05:24:32Z

Claim your assigned genome

← Older revision		Revision as of 05:24, 23 May 2014
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	\| 1102 \|\| YBT \|\| B. hermsii (?) \|\| Relapsing Fever \|\|		\| 1102 \|\| YBT \|\| B. hermsii (?) \|\| Relapsing Fever \|\|
	* [http://www.ncbi.nlm.nih.gov/nuccore/CP005706.1 main chromosome]		* [http://www.ncbi.nlm.nih.gov/nuccore/CP005706.1 main chromosome]
			\|\|
			* Accession: CP005706; Assigned to: ?
			\|-
			\| ?? \|\| SLO \|\| B. parkeri (?) \|\| Relapsing Fever \|\|
			* [http://www.ncbi.nlm.nih.gov/nuccore/CP005851.1 main chromosome]
	\|\|		\|\|
	* Accession: CP005706; Assigned to: ?		* Accession: CP005706; Assigned to: ?

imported>Weigang: /* Claim your assigned genome */

2014-03-31T18:42:08Z

Claim your assigned genome

@@ Line 72: / Line 72: @@
 ||
 * Accession: CP000048; Assigned to: KR
 |-
 | 1200 || 91E135 || B. turicatae (Texas) || Relapsing Fever ||

imported>Weigang: /* Part 3. Generate database tables & deposit your results */

2014-03-11T20:25:17Z

Part 3. Generate database tables & deposit your results

← Older revision		Revision as of 20:25, 11 March 2014
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	==Part 3. Generate database tables & deposit your results==		==Part 3. Generate database tables & deposit your results==
	* '''Note: Use your assigned genome_id in the table above as the argument for the "-g" option'''		* '''Note: Use your assigned genome_id in the table above as the argument for the "-g" option'''
	<syntaxhighlight lang="bash" line start="10" enclose="div">		<syntaxhighlight lang="bash" line start="12" enclose="div">
	./gb2table.pl -g <genome_id> -c <accession.gb> # Expected output: "accession.contig.txt"		./gb2table.pl -g <genome_id> -c <accession.gb> # Expected output: "accession.contig.txt"
	./gb2table.pl -g <genome_id> -f <accession.gb> # Expected output: "accession.orf.txt"		./gb2table.pl -g <genome_id> -f <accession.gb> # Expected output: "accession.orf.txt"

imported>Weigang: /* Part 2. Predict orthologs with reciprocal BLAST */

2014-03-11T20:23:16Z

Part 2. Predict orthologs with reciprocal BLAST

← Older revision		Revision as of 20:23, 11 March 2014
Line 125:		Line 125:
	blastp -query accession.pep -db ref -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.fwd # Forward BLAST # customized outfmt 6		blastp -query accession.pep -db ref -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.fwd # Forward BLAST # customized outfmt 6
	blastp -query b31.pep -db mygenome -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.rev # Reverse BLAST		blastp -query b31.pep -db mygenome -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.rev # Reverse BLAST
	./find-reciprocal.pl <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # Identify orthologs.		./find-reciprocal.pl <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # Identify orthologs.
	.~~/find-reciprocal.pl~~ -d 80 ~~<accession.fwd> <accession.rev> >~~ accession.orthlogs 2> accession.not-orthologs ~~# for replasping-fever genomes~~		# check results. If orthologs less than 90% of total ORFs in genbank file, run the previous command with more relaxed stringency (use "-d 80", 80% identify cutoff)
			wc accession.orthlogs
			wc accession.not-orthologs
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang: /* Part 3. Generate database tables & deposit your results */

2014-03-11T20:20:40Z

Part 3. Generate database tables & deposit your results

← Older revision		Revision as of 20:20, 11 March 2014
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	* '''Note: Use your assigned genome_id in the table above as the argument for the "-g" option'''		* '''Note: Use your assigned genome_id in the table above as the argument for the "-g" option'''
	<syntaxhighlight lang="bash" line start="10" enclose="div">		<syntaxhighlight lang="bash" line start="10" enclose="div">
	./gb2table.pl -g <genome_id> -t <accession.gb> # Expected output: "accession.contig.txt"		./gb2table.pl -g <genome_id> -c <accession.gb> # Expected output: "accession.contig.txt"
	./gb2table.pl -g <genome_id> -f <accession.gb> # Expected output: "accession.orf.txt"		./gb2table.pl -g <genome_id> -f <accession.gb> # Expected output: "accession.orf.txt"
			# Check your outputs
			wc <accession.contig.txt>
			head <accession.contig.txt>
			tail <accession.contig.txt>
			wc <accession.orf.txt>
			head <accession.orf.txt>
			tail <accession.orf.txt>
	cp accession.contig.txt ../../bio425/annotate-a-genome-results/your_initial.accession.contig.txt		cp accession.contig.txt ../../bio425/annotate-a-genome-results/your_initial.accession.contig.txt
	cp accession.orf.txt ../../bio425/annotate-a-genome-results/your_initial.accession.orf.txt		cp accession.orf.txt ../../bio425/annotate-a-genome-results/your_initial.accession.orf.txt

imported>Weigang: /* Part 3. Generate database tables & deposit your results */

2014-03-09T06:10:04Z

Part 3. Generate database tables & deposit your results

← Older revision		Revision as of 06:10, 9 March 2014
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	cp accession.contig.txt ../../bio425/annotate-a-genome-results/your_initial.accession.contig.txt		cp accession.contig.txt ../../bio425/annotate-a-genome-results/your_initial.accession.contig.txt
	cp accession.orf.txt ../../bio425/annotate-a-genome-results/your_initial.accession.orf.txt		cp accession.orf.txt ../../bio425/annotate-a-genome-results/your_initial.accession.orf.txt
	cp accession.~~orth~~ ../../bio425/annotate-a-genome-results/your_initial.accession.orth		cp accession.orthologs ../../bio425/annotate-a-genome-results/your_initial.accession.orth
	cp accession.not-~~orth~~ ../../bio425/annotate-a-genome-results/your_initial.accession.not-~~orht~~		cp accession.not-orthologs ../../bio425/annotate-a-genome-results/your_initial.accession.not-orth
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang: /* Part 3. Generate database tables */

2014-03-09T06:09:26Z

Part 3. Generate database tables

← Older revision		Revision as of 06:09, 9 March 2014
Line 129:		Line 129:
	</syntaxhighlight>		</syntaxhighlight>

	==Part 3. Generate database tables==		==Part 3. Generate database tables & deposit your results==
	* '''Note: Use your assigned genome_id in the table above as the argument for the "-g" option'''		* '''Note: Use your assigned genome_id in the table above as the argument for the "-g" option'''
	<syntaxhighlight lang="bash" line start="10" enclose="div">		<syntaxhighlight lang="bash" line start="10" enclose="div">
	./gb2table.pl -g <genome_id> -t <accession.gb> # Expected output: "accession.contig.txt"		./gb2table.pl -g <genome_id> -t <accession.gb> # Expected output: "accession.contig.txt"
	./gb2table.pl -g <genome_id> -f <accession.gb> # Expected output: "accession.orf.txt"		./gb2table.pl -g <genome_id> -f <accession.gb> # Expected output: "accession.orf.txt"
	cp accession.contig.txt accession.orf.txt accession.orth accession.no-orth		cp accession.contig.txt ../../bio425/annotate-a-genome-results/your_initial.accession.contig.txt
			cp accession.orf.txt ../../bio425/annotate-a-genome-results/your_initial.accession.orf.txt
			cp accession.orth ../../bio425/annotate-a-genome-results/your_initial.accession.orth
			cp accession.not-orth ../../bio425/annotate-a-genome-results/your_initial.accession.not-orht
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang: /* Part 3. Generate database tables */

2014-03-09T05:59:47Z

Part 3. Generate database tables

← Older revision		Revision as of 05:59, 9 March 2014
Line 131:		Line 131:
	==Part 3. Generate database tables==		==Part 3. Generate database tables==
	* '''Note: Use your assigned genome_id in the table above as the argument for the "-g" option'''		* '''Note: Use your assigned genome_id in the table above as the argument for the "-g" option'''
	<syntaxhighlight lang="bash" line start="7" enclose="div">		<syntaxhighlight lang="bash" line start="10" enclose="div">
	./gb2table.pl -g <genome_id> -t <accession.gb> # Expected output: "accession.contig.txt"		./gb2table.pl -g <genome_id> -t <accession.gb> # Expected output: "accession.contig.txt"
	./gb2table.pl -g <genome_id> -f <accession.gb> # Expected output: "accession.orf.txt"		./gb2table.pl -g <genome_id> -f <accession.gb> # Expected output: "accession.orf.txt"
			cp accession.contig.txt accession.orf.txt accession.orth accession.no-orth
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang: /* Part 2. Predict orthologs with reciprocal BLAST */

2014-03-09T05:54:35Z

Part 2. Predict orthologs with reciprocal BLAST

← Older revision		Revision as of 05:54, 9 March 2014
Line 120:		Line 120:
	* Commands:		* Commands:
	<syntaxhighlight lang="bash" line start="3" enclose="div">		<syntaxhighlight lang="bash" line start="3" enclose="div">
	makeblastdb -in accession.pep -dbtype 'prot' -parse_seqids # Prepare the new genome DB		cp ../../bio425/annotate-genome-pipeline/b31.pep . # get reference genome
			makeblastdb -in b31.pep -dbtype 'prot' -parse_seqids -out ref # Prepare the ref genome DB
			makeblastdb -in accession.pep -dbtype 'prot' -parse_seqids -out mygenome # Prepare the new genome DB
	blastp -query accession.pep -db ref -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.fwd # Forward BLAST # customized outfmt 6		blastp -query accession.pep -db ref -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.fwd # Forward BLAST # customized outfmt 6
	blastp -query ~~GBB~~.pep -db ~~accession.pep~~ -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.rev # Reverse BLAST		blastp -query b31.pep -db mygenome -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.rev # Reverse BLAST
	./find-reciprocal.pl <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # Identify orthologs.		./find-reciprocal.pl <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # Identify orthologs.
	./find-reciprocal.pl -d 80 <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # for replasping-fever genomes		./find-reciprocal.pl -d 80 <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # for replasping-fever genomes

imported>Weigang: /* Part 2. Predict orthologs with reciprocal BLAST */

2014-03-09T05:38:07Z

Part 2. Predict orthologs with reciprocal BLAST

← Older revision		Revision as of 05:38, 9 March 2014
Line 116:		Line 116:

	==Part 2. Predict orthologs with reciprocal BLAST==		==Part 2. Predict orthologs with reciprocal BLAST==
	* '''Note: Replace the "accession" in the following commands with your assigned accession number.'''		* '''Note 1: Replace the "accession" in the following commands with your assigned accession number.'''
			* '''Note 2: You may have to lower the identity (-d, default 90) and length coverage (-l, default 90) for replapsing fever genomes'''
	* Commands:		* Commands:
	<syntaxhighlight lang="bash" line start="3" enclose="div">		<syntaxhighlight lang="bash" line start="3" enclose="div">
	makeblastdb -in accession.pep -dbtype 'prot' -parse_seqids # Prepare the new genome DB		makeblastdb -in accession.pep -dbtype 'prot' -parse_seqids # Prepare the new genome DB
	blastp -query accession.pep -db ref -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.fwd # Forward BLAST # customized outfmt 6		blastp -query accession.pep -db ref -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.fwd # Forward BLAST # customized outfmt 6
	blastp -query ~~ref~~.pep -db accession.pep -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.rev # Reverse BLAST		blastp -query GBB.pep -db accession.pep -outfmt '6 qseqid sseqid pident length qlen evalue' -evalue 1e-3 -out accession.rev # Reverse BLAST
	./~~check~~-reciprocal.pl <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # Identify orthologs		./find-reciprocal.pl <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # Identify orthologs.
			./find-reciprocal.pl -d 80 <accession.fwd> <accession.rev> > accession.orthlogs 2> accession.not-orthologs # for replasping-fever genomes
	</syntaxhighlight>		</syntaxhighlight>