Wikiomics:Bioinfo tutorial - Revision history

Darek Kedra: /* Similarity plots (dot-plots) */

2012-11-21T20:26:17Z

Similarity plots (dot-plots)

←Older revision		Revision as of 20:26, 21 November 2012
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	Note that the order of DNA vs protein comparison matters. Try to keep sequence names within your multiple_fasta file short.		Note that the order of DNA vs protein comparison matters. Try to keep sequence names within your multiple_fasta file short.

		+	Scaling down image 10x with -z option:
		+	<pre>
		+	dotter first_fasta_DNA.seq second_fasta_DNA.seq -z 10
		+	</pre>
		+
		+
		+	Detailed description how to add annotation to dotplots:
		+	[http://bioinformatics.abc.hu/tothg/biocomp/other/Dotter.html]
		+
		+	The example format of sequence features file (passed with -f option to dotter)
		+	<pre>
		+	100 @1 CDS 1 1124 RED gene1
		+	100 @1 CDS 3360 3965 RED gene2
		+	100 @1 CDS 3360 3968 RED gene3
		+	</pre>
	* [http://bioweb.pasteur.fr/docs/EMBOSS/dottup.html dottup info] (Emboss, Unix/Web) [http://bioweb.pasteur.fr/seqanal/interfaces/dottup.html web form]		* [http://bioweb.pasteur.fr/docs/EMBOSS/dottup.html dottup info] (Emboss, Unix/Web) [http://bioweb.pasteur.fr/seqanal/interfaces/dottup.html web form]

Darek Kedra: /* Tree display */

2011-06-24T14:08:05Z

Tree display

←Older revision		Revision as of 14:08, 24 June 2011
Line 717:		Line 717:

	===Tree display===		===Tree display===
		+	For the comprehensive list see:
		+	http://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software
		+
	* [http://iubio.bio.indiana.edu/treeapp/treeprint-form.html Phylodendron]		* [http://iubio.bio.indiana.edu/treeapp/treeprint-form.html Phylodendron]
	* [http://pbil.univ-lyon1.fr/software/njplot.html njplot]		* [http://pbil.univ-lyon1.fr/software/njplot.html njplot]

Darek Kedra: /* Sequence/structure retrieval */

2011-04-18T12:02:33Z

Sequence/structure retrieval

←Older revision		Revision as of 12:02, 18 April 2011
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	==Sequence/structure retrieval==		==Sequence/structure retrieval==
	* [http://www.ncbi.nlm.nih.gov/Entrez/ '''Entrez''' ]		* [http://www.ncbi.nlm.nih.gov/Entrez/ '''Entrez''' ]
-	* [http://www.ncbi.nlm.nih.gov/~~entrez~~/batchentrez~~.cgi?db=Nucleotide~~ '''Batch Entrez''' ] (retrieving multiple DNA/protein entries at once):	+	* [http://www.ncbi.nlm.nih.gov/sites/batchentrez '''Batch Entrez''' ] (retrieving multiple DNA/protein entries at once):
	* [http://srs.ebi.ac.uk/ '''SRS''' ] (complex queries )		* [http://srs.ebi.ac.uk/ '''SRS''' ] (complex queries )
	* [http://webclu.bio.wzw.tum.de/prompt/index.php PROMPT] Protein Mapping and Comparison Tool		* [http://webclu.bio.wzw.tum.de/prompt/index.php PROMPT] Protein Mapping and Comparison Tool

Darek Kedra: /* HMM and profile searches */

2010-09-16T15:18:47Z

HMM and profile searches

←Older revision		Revision as of 15:18, 16 September 2010
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	hmmsearch your_ALIGNED_sequences.hmm protein_database.fasta		hmmsearch your_ALIGNED_sequences.hmm protein_database.fasta
	</pre>		</pre>
		+
		+	in HMMER3 you have to specify the format, i.e.
		+	<pre>
		+	/hmmbuild --amino --informat afa --cpu 8 your_ALIGNED_sequences.hmm your_ALIGNED_sequences.fasta
		+	</pre>
		+

	** MEME MAST [ http://meme.sdsc.edu/]		** MEME MAST [ http://meme.sdsc.edu/]

Darek Kedra: /* Genome annotation using ESTs assembly */

2010-05-05T08:40:36Z

Genome annotation using ESTs assembly

←Older revision		Revision as of 08:40, 5 May 2010
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	===Genome annotation using ESTs assembly===		===Genome annotation using ESTs assembly===

-	* [http://~~www~~.~~tigr~~.~~org~~/~~tdb/e2k1/ath1/pasa_annot_updates/pasa_annot_updates.shtml~~ PASA~~@TIGR~~]	+	* [http://pasa.sourceforge.net/ PASA] tool used in many current genome annotation projects

	==Synthetic genes==		==Synthetic genes==

Darek Kedra: - dead link

2010-04-09T09:18:21Z

- dead link

←Older revision		Revision as of 09:18, 9 April 2010
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	* [http://www.thebiogrid.org BioGRID]		* [http://www.thebiogrid.org BioGRID]
	* [http://mips.gsf.de/proj/ppi/ Mammalian Protein-Protein Interaction Database @MIPS]		* [http://mips.gsf.de/proj/ppi/ Mammalian Protein-Protein Interaction Database @MIPS]
-	~~<!--- broken link [http://interweaver.i2r.a-star.edu.sg/exp/ Interweaver] protein sequence searches for orthologues and their interactions~~
-	~~--->~~
	* [http://stitch.embl.de/ STITCH] Chemical-Protein Interactions		* [http://stitch.embl.de/ STITCH] Chemical-Protein Interactions

Darek Kedra: /* Vector masking */ +Figaro

2010-03-23T16:29:06Z

Vector masking: +Figaro

←Older revision		Revision as of 16:29, 23 March 2010
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	You will get a file: fasta_file_to_be_masked.screen without the sequences matching masking_sequence.		You will get a file: fasta_file_to_be_masked.screen without the sequences matching masking_sequence.
		+
		+	* Figaro
		+	A novel approach for finding putative vector/adapter sequences without knowledge of the vector sequence.
		+	"vector sequence is automatically inferred by analyzing the frequency of occurrence of short oligo-nucleotides using Poisson statistics"
		+	http://sourceforge.net/apps/mediawiki/amos/index.php?title=Figaro

	==Masking repetitive sequences using RepeatMasker (WWW/Unix)==		==Masking repetitive sequences using RepeatMasker (WWW/Unix)==

Darek Kedra: /* Masking repetitive sequences using RepeatMasker (WWW/Unix) */

2010-03-22T14:45:01Z

Masking repetitive sequences using RepeatMasker (WWW/Unix)

←Older revision		Revision as of 14:45, 22 March 2010
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	You will get a file: fasta_file_to_be_masked.screen without the sequences matching masking_sequence.		You will get a file: fasta_file_to_be_masked.screen without the sequences matching masking_sequence.

-	===Masking repetitive sequences using RepeatMasker (WWW/Unix)===	+	==Masking repetitive sequences using RepeatMasker (WWW/Unix)==

-	* ~~Online~~: [http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker]	+	* web site: http://www.repeatmasker.org/
		+	* current version (checked on 2010-03.22): 3.2.8
		+	* documentation: http://www.repeatmasker.org/webrepeatmaskerhelp.html
		+
		+
		+	* Online web server [http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker]

	* command line		* command line
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	repmask your_sequence_in_fasta_format		repmask your_sequence_in_fasta_format
	</pre>		</pre>
		+
	You will get a file: your_sequence_in_fasta_format.masked --- name tells all		You will get a file: your_sequence_in_fasta_format.masked --- name tells all

Darek Kedra: /* Methods */ spell

2010-03-22T11:19:19Z

Methods: spell

←Older revision		Revision as of 11:19, 22 March 2010
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	* distance methods		* distance methods
-	** ~~Neighbour~~ joining NJ	+	** Neighbor joining NJ
-	** UPGMA (Unweighted Pair Group Method with Arithmetic mean) assumes rate of mutation constant along branches of a tree. Less ~~acurate~~ for sequence data than NJ.	+	** UPGMA (Unweighted Pair Group Method with Arithmetic mean) assumes rate of mutation constant along branches of a tree. Less accurate for sequence data than NJ.

-	* maximum likehood (~~computationaly~~ intense, but more accurate)	+	* maximum likehood (computationally intense, but more accurate)


-	To check ~~validy~~ of a tree:	+	To check validity of a tree:
	* bootstrap		* bootstrap
-	After creating a tree from MSA ~~bootstraping~~ program selects number of columns from MSA and calculates a tree. ~~Thsi~~ process is repeated 100-1000 times and resulting trees are compared with previously created one. Branches present in more than 70% of bootstrap samples are believed to have a good support.	+	After creating a tree from MSA bootstrapping program selects number of columns from MSA and calculates a tree. This process is repeated 100-1000 times and resulting trees are compared with previously created one. Branches present in more than 70% of bootstrap samples are believed to have a good support.
	These estimates are conservative		These estimates are conservative
	<!-- * jackknife ??parsimony jackknife -->		<!-- * jackknife ??parsimony jackknife -->

Darek Kedra: links to blast tutorials

2010-03-19T13:23:11Z

links to blast tutorials

←Older revision		Revision as of 13:23, 19 March 2010
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	===First tier algorithms===		===First tier algorithms===
	* '''Blast''' [http://www.ncbi.nlm.nih.gov/BLAST/ ]		* '''Blast''' [http://www.ncbi.nlm.nih.gov/BLAST/ ]
		+	For the detailed BLAST tutorial see [[Wikiomics:BLAST_tutorial]]

	Warning: There is a major change of blast standalone binaries. Info below is describing blastall based programs. While most of the options will work with new blast+ , check the information		Warning: There is a major change of blast standalone binaries. Info below is describing blastall based programs. While most of the options will work with new blast+ , check the information
Line 1,128:		Line 1,129:

	Also there are relevant pages on Wikiomics web site:		Also there are relevant pages on Wikiomics web site:
		+	* [[Wikiomics:BLAST_tutorial]]
		+
	* [[Wikiomics:Bioinformatics courses(external)]]		* [[Wikiomics:Bioinformatics courses(external)]]

	* [[Wikiomics:SRS_tutorials]]		* [[Wikiomics:SRS_tutorials]]
	* [[Wikiomics:Ensembl_tutorials]]		* [[Wikiomics:Ensembl_tutorials]]
		+
	* [[Wikiomics:Staden]]		* [[Wikiomics:Staden]]
	* [[Wikiomics:Cloning_in_silico]]		* [[Wikiomics:Cloning_in_silico]]