Recent changes to Input Formats

Input Formats modified by Mathias Kuhring

Mathias Kuhring — Mon, 12 Jan 2015 14:08:45 -0000

Input Formats modified by Mathias Kuhring

Mathias Kuhring — Mon, 12 Jan 2015 14:08:20 -0000

--- v6
+++ v7
@@ -75,7 +75,7 @@

 Proteome fasta file (optional)
 ------------------------------
-The mapping might be supported by a proteome fasta, e.g. with those proteins used for the peptide identifications. For the human PSMs example you can just download the human proteome in fasta format from the Uniprot FTP server (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/).
+The id mapping might be supported by the headers in a proteome fasta file, e.g. with those proteins used for the peptide identifications. For the human PSMs example you can just download the human proteome in fasta format from the Uniprot FTP server (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/).

 The data in the file should look like this:

WikiPage Input Formats modified by Mathias Kuhring

Mathias Kuhring — Thu, 29 Mar 2012 11:18:41 -0000

WikiPage Data Formats modified by Mathias Kuhring

Mathias Kuhring — Mon, 19 Mar 2012 14:27:39 -0000

--- v4 
+++ v5 
@@ -10,7 +10,7 @@
 iPiG will import every "PeptideEvidence" element from the "SpectrumIdentificationItem" elements pooled with necessary information from the referenced peptides ("Peptide_ref" attribute) and proteins ("DBSequence_Ref" attribute) which are the peptide sequences and modification as well as protein accessions and descriptions.
 
 As an **alternative** to the mzIdentML format, iPiG can import a simple tab-separated text file. E.g. such files can be extract from Mascot Search Results as CSV files
-by removing those columns which are not included in the example below.
+by removing all header lines except the column titles and removing those columns which are not included in the example below.
 
 Please note, the names and order of the remaining columns are important since these files are verified by their header line. In addition, sometimes it may be necessary to add some columns manually, e.g. "pep_isunique"

WikiPage Data Formats modified by Mathias Kuhring

Mathias Kuhring — Mon, 19 Mar 2012 13:12:07 -0000

--- v3 
+++ v4 
@@ -1,94 +1,94 @@
-For the mapping of peptide spectrum matches (PSMs) to the genome you will need a file with your PSMs of interest and some files containing information about gene locations and protein-gene connections, as described below.
-
-In generel, you will find example files of some data descript here in the "examples" folder coming with the tool (except mzIdentML and chromosome files). Please note, they are just excerpts, thus not suitable for real usage.
-
+For the mapping of peptide spectrum matches (PSMs) to the genome a file with the PSMs of interest and some files containing information about gene locations and protein-gene connections are required as described below.
+
+In general, example files are provide in the "examples" folder coming with the tool (except for mzIdentML and chromosome files). Please note, they are just excerpts to exemplify the format, they are not suitable for actual meaningful usage.
+
 Peptide spectrum matches
 ------------------------
 The PSMs of interest should be provided in the **mzIdentML** format (*.mzid) which is a XML based standard specific for peptide and protein identifications from mass spectra. The integrity of the input file will be checked with a XML schema (currently: mzIdentML1.0.0.xsd). 
-For more details about the format and some example files visit the webpage ot the HUPO Proteomics Standards Initiative (http://www.psidev.info/index.php?q=node/403).
-
-For your information, iPiG will import every "PeptideEvidence" element from the "SpectrumIdentificationItem" elements pooled with necessary information from the referenced peptides ("Peptide_ref" attribute) and proteins ("DBSequence_Ref" attribute) which are the peptide sequences and modification as well as protein accessions and descriptions.
-
-As an **alternative** to the mzIdentML format, iPiG can import a simple tab-separated text file. E.g. you can extract such files from Mascot Search Results exported as CSV files
-by removing all header lines except the column titles and removing those columns which are not included in the example below.
-
-Please note, the names and order of the remaing columns are importened, since these files are verified by the header. In addition, sometimes it seems to be necessary to add some columns manually, e.g. "pep_isunique"
+For more details about the format and some example files visit the webpage at the HUPO Proteomics Standards Initiative (http://www.psidev.info/index.php?q=node/403).
+
+iPiG will import every "PeptideEvidence" element from the "SpectrumIdentificationItem" elements pooled with necessary information from the referenced peptides ("Peptide_ref" attribute) and proteins ("DBSequence_Ref" attribute) which are the peptide sequences and modification as well as protein accessions and descriptions.
+
+As an **alternative** to the mzIdentML format, iPiG can import a simple tab-separated text file. E.g. such files can be extract from Mascot Search Results as CSV files
+by removing those columns which are not included in the example below.
+
+Please note, the names and order of the remaining columns are important since these files are verified by their header line. In addition, sometimes it may be necessary to add some columns manually, e.g. "pep_isunique"
 
 The data in the text file should look like this:
 
     prot_acc	prot_desc	pep_query	pep_isunique	pep_exp_z	pep_score	pep_seq	pep_var_mod	pep_var_mod_pos
     CPSM_HUMAN	Carbamoyl-phosphate synthase ammonia, mitochondrial OS=Homo sapiens GN=CPS1 PE=1 SV=2	99	1	2	5.36	ASRSFPFVSK
     FAS_HUMAN	Fatty acid synthase OS=Homo sapiens GN=FASN PE=1 SV=3	149	1	2	60.67	VGDPQELNGITR
 

 
 Gene Annotations
 ----------------
-As gene annotations UCSC and Ensembl genes in the UCSC table format (tab-separated) are supported yet, thus the UCSC Table Browser is recommanded as source (http://genome.ucsc.edu/cgi-bin/hgTables?command=start).
-
-E.g. if you like map peptide spectrum matches (PSMs) obtained from a human sample, go to the Table Browser and use the following settings:
+As gene annotations UCSC and Ensembl genes in the UCSC table format (tab-separated) are currently supported, thus the UCSC Table Browser is recommended as source (http://genome.ucsc.edu/cgi-bin/hgTables?command=start).
+
+E.g. if mapping peptide spectrum matches (PSMs) obtained from a human sample, we recommend going to the Table Browser and using the following settings:
 clade: "Mammal", genome: "Human", assembly: "Feb. 2009 (GRCh37/hg19)" (resp. the latest),
 group: "Genes and Gene Prediction Tracks", track: "UCSC Genes" or "Ensembl Genes"
 table: "knownGene" resp. "ensGene", region: "genome", output format: "all fields from selected table"
 Indicate a file name (*.txt) in the field "output file" and download the file via the "get output" button.
 
 The data in the file should look like this:
 
     Example UCSC Genes:
     #name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	proteinID	alignID
     uc009vjk.2	chr1	+	322036	326938	324342	325605	3	322036,324287,324438,	322228,324345,326938,	C9J4L2	uc009vjk.2
     uc001aau.3	chr1	+	323891	328581	324342	325605	3	323891,324287,324438,	324060,324345,328581,	C9J4L2	uc001aau.3
     Example Ensemble Genes:
     #bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
     9	ENST00000472741	chr1	-	1026425	1051467	1051467	1051467	3	1026425,1027370,1051439,	1026945,1027483,1051467,	0	ENSG00000131591	none	none	-1,-1,-1,
     34	ENST00000478275	chr1	-	212859759	212872097	212872097	212872097	2	212859759,212870302,	212860321,212872097,	0	ENSG00000123685	none	none	-1,-1,
 

 
 Amino Acid Sequences
 --------------------
 The amino acid sequences have to correspond to the gene annotations, therefore they have to be in the UCSC table format (tab-separated) as well.
-Oviously, the UCSC Table Browser is a recommanded source for this data, too (http://genome.ucsc.edu/cgi-bin/hgTables?command=start).
+The UCSC Table Browser is a recommended source for this data, too (http://genome.ucsc.edu/cgi-bin/hgTables?command=start).
 
 E.g. following the example with human PSMs, the parameters are mainly the same, except one field:
 table: "knownGenePep" resp. "ensPep"
-Just save the data like descripted above.
+Saving the data can be accomplished as described above.
 
 The data in the file should look like this:
 
     Example UCSC Genes:
     #name	seq
     uc010nxq.1	    MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCLPSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH
     uc001adj.1	MQRWIMEKTAEHFQEAMEESKTHFRAVDPDGDGHVSWDEYKVKFLASKGHSEKEVADAIRLNEELKVDEESECSARLPPPVSGILCVRACVVCT
     Example Ensemble Genes:
     #name	seq
     ENST00000004921	MKGLAAALLVLVCTMALCSCAQVGTNKELCCLVYTSWQIPQKFIVDYSETSPQCPKPGVILLTKRGRQICADPNKKWVQKYISDLKLNA
     ENST00000005180	MMGLSLASAVLLASLLSLHLGTATRGSDISKTCCFQYSHKPLPWTWVRSYEFTSNSCSQRAVIFTTKRGKKVCTHPRKKWVQKYISLLKTPKQL
 

 
 Uniprot ID-mapping file (optional, but recommended)
 ---------------------------------------------------
-For the id mapping only the Uniprot ID-mapping file with tab-separation is supported yet. It can be downloaded from the Uniprot FTP for several species
+For the id mapping only the Uniprot ID-mapping file with tab-separation is currently supported. It can be downloaded from the Uniprot FTP for several species
 (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/).
 
 E.g. for a Human ID-mapping file, browse the FTP directory, change to the "by organism" directory and download the corresponding tab-file (like "HUMAN*.tab").
-For an example open "examples\Uniprot_idmapping.tab" with a text editor.
+For an example, open "examples\Uniprot_idmapping.tab" with a text editor.
 
 
 Proteome fasta file (optional)
 ------------------------------
-The mapping might be supported by a proteome fasta, e.g. with those proteins used for the peptide identifications. In general, a recommanded source for proteoms is the Uniprot database, e.g. their FTP (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/). For the human PSMs example you can just download the human proteome in fasta format from the Uniprot FTP server.
+The mapping might be supported by a proteome fasta, e.g. with those proteins used for the peptide identifications. For the human PSMs example you can just download the human proteome in fasta format from the Uniprot FTP server (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/).
 
 The data in the file should look like this:
 
     >sp|A0A183|LCE6A_HUMAN Late cornified envelope protein 6A OS=Homo sapiens GN=LCE6A PE=2 SV=1
     MSQQKQQSWKPPNVPKCSPPQRSNPCLAPYSTPCGAPHSEGCHSSSQRPEVQKPRRARQK
     LRCLSRGTTYHCKEEECEGD
     >tr|A0A4R5|A0A4R5_HUMAN Keratin 19 (Fragment) OS=Homo sapiens GN=keratin 19 PE=2 SV=1
     TIENARIVLQINNAQLAADDF
 

 
 Reference Chromosomes (for GeneControl)
 ---------------------------------------
-If you are going to use the GeneControl, you will need a set of reference chromosomes (resp. scaffolds) covering all the genes in the annotation file. You have to provide a fasta file (*.fa!) for each chromosome in one folder, whereby the file names must correspond to the chromosome names in the annotations (e.g. chr1.fa, chrX.fa, chrIV.fa, etc.).
+For using the GeneControl, a set of reference chromosomes (resp. scaffolds) covering all the genes in the annotation file is required. A fasta file (*.fa!) has to be provided for each chromosome in a single folder, whereby the file names must correspond to the chromosome names in the annotations (e.g. chr1.fa, chrX.fa, chrIV.fa, etc.).
 Again, UCSC is a good source for the data (http://hgdownload.cse.ucsc.edu/downloads.html).
 
-E.g. to get a human chromosome reference set, choose "human" from the vertebrates at the suggested download site, continue with "Full data set" and download the "chromFa.tar.gz" file from the button of the page. Extract the archive to folder of your choice which you can indicated in the GeneControl later.
+E.g. to get a human chromosome reference set, choose "human" from the vertebrates at the suggested download site, continue with "Full data set" and download the "chromFa.tar.gz" file from the button of the page. Extract the archive to a folder of choice which can be indicated in the GeneControl later.

WikiPage Data Formats modified by Mathias Kuhring

Mathias Kuhring — Sat, 17 Mar 2012 07:10:49 -0000

--- v2 
+++ v3 
@@ -5,7 +5,7 @@
 Peptide spectrum matches
 ------------------------
 The PSMs of interest should be provided in the **mzIdentML** format (*.mzid) which is a XML based standard specific for peptide and protein identifications from mass spectra. The integrity of the input file will be checked with a XML schema (currently: mzIdentML1.0.0.xsd). 
-For more details about the format visit the webpage ot the HUPO Proteomics Standards Initiative (http://www.psidev.info/index.php?q=node/403).
+For more details about the format and some example files visit the webpage ot the HUPO Proteomics Standards Initiative (http://www.psidev.info/index.php?q=node/403).
 
 For your information, iPiG will import every "PeptideEvidence" element from the "SpectrumIdentificationItem" elements pooled with necessary information from the referenced peptides ("Peptide_ref" attribute) and proteins ("DBSequence_Ref" attribute) which are the peptide sequences and modification as well as protein accessions and descriptions.

WikiPage Data Formats modified by Mathias Kuhring

Mathias Kuhring — Fri, 16 Mar 2012 18:39:25 -0000

--- v1 
+++ v2 
@@ -16,76 +16,79 @@
 
 The data in the text file should look like this:
 
-prot_acc | prot_desc | pep_query | pep_isunique | pep_exp_z | pep_score | pep_seq | pep_var_mod | pep_var_mod_pos
-
-prot_acc	prot_desc	pep_query	pep_isunique	pep_exp_z	pep_score	pep_seq	pep_var_mod	pep_var_mod_pos
-CPSM_HUMAN	Carbamoyl-phosphate synthase ammonia, mitochondrial OS=Homo sapiens GN=CPS1 PE=1 SV=2	99	1	2	5.36	ASRSFPFVSK		
-FAS_HUMAN	Fatty acid synthase OS=Homo sapiens GN=FASN PE=1 SV=3	149	1	2	60.67	VGDPQELNGITR	
-
-
-2.) Gene Annotations
+    prot_acc	prot_desc	pep_query	pep_isunique	pep_exp_z	pep_score	pep_seq	pep_var_mod	pep_var_mod_pos
+    CPSM_HUMAN	Carbamoyl-phosphate synthase ammonia, mitochondrial OS=Homo sapiens GN=CPS1 PE=1 SV=2	99	1	2	5.36	ASRSFPFVSK
+    FAS_HUMAN	Fatty acid synthase OS=Homo sapiens GN=FASN PE=1 SV=3	149	1	2	60.67	VGDPQELNGITR
+

+
+Gene Annotations
+----------------
 As gene annotations UCSC and Ensembl genes in the UCSC table format (tab-separated) are supported yet, thus the UCSC Table Browser is recommanded as source (http://genome.ucsc.edu/cgi-bin/hgTables?command=start).
 
 E.g. if you like map peptide spectrum matches (PSMs) obtained from a human sample, go to the Table Browser and use the following settings:
 clade: "Mammal", genome: "Human", assembly: "Feb. 2009 (GRCh37/hg19)" (resp. the latest),
 group: "Genes and Gene Prediction Tracks", track: "UCSC Genes" or "Ensembl Genes"
 table: "knownGene" resp. "ensGene", region: "genome", output format: "all fields from selected table"
 Indicate a file name (*.txt) in the field "output file" and download the file via the "get output" button.
 
 The data in the file should look like this:
-Example UCSC Genes:
-#name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	proteinID	alignID
-uc009vjk.2	chr1	+	322036	326938	324342	325605	3	322036,324287,324438,	322228,324345,326938,	C9J4L2	uc009vjk.2
-uc001aau.3	chr1	+	323891	328581	324342	325605	3	323891,324287,324438,	324060,324345,328581,	C9J4L2	uc001aau.3
-Example Ensemble Genes:
-#bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
-9	ENST00000472741	chr1	-	1026425	1051467	1051467	1051467	3	1026425,1027370,1051439,	1026945,1027483,1051467,	0	ENSG00000131591	none	none	-1,-1,-1,
-34	ENST00000478275	chr1	-	212859759	212872097	212872097	212872097	2	212859759,212870302,	212860321,212872097,	0	ENSG00000123685	none	none	-1,-1,
-
-3.) Amino Acid Sequences
+
+    Example UCSC Genes:
+    #name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	proteinID	alignID
+    uc009vjk.2	chr1	+	322036	326938	324342	325605	3	322036,324287,324438,	322228,324345,326938,	C9J4L2	uc009vjk.2
+    uc001aau.3	chr1	+	323891	328581	324342	325605	3	323891,324287,324438,	324060,324345,328581,	C9J4L2	uc001aau.3
+    Example Ensemble Genes:
+    #bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
+    9	ENST00000472741	chr1	-	1026425	1051467	1051467	1051467	3	1026425,1027370,1051439,	1026945,1027483,1051467,	0	ENSG00000131591	none	none	-1,-1,-1,
+    34	ENST00000478275	chr1	-	212859759	212872097	212872097	212872097	2	212859759,212870302,	212860321,212872097,	0	ENSG00000123685	none	none	-1,-1,
+

+
+Amino Acid Sequences
+--------------------
 The amino acid sequences have to correspond to the gene annotations, therefore they have to be in the UCSC table format (tab-separated) as well.
 Oviously, the UCSC Table Browser is a recommanded source for this data, too (http://genome.ucsc.edu/cgi-bin/hgTables?command=start).
 
 E.g. following the example with human PSMs, the parameters are mainly the same, except one field:
 table: "knownGenePep" resp. "ensPep"
 Just save the data like descripted above.
 
 The data in the file should look like this:
-Example UCSC Genes:
-#name	seq
-uc010nxq.1	MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCLPSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH
-uc001adj.1	MQRWIMEKTAEHFQEAMEESKTHFRAVDPDGDGHVSWDEYKVKFLASKGHSEKEVADAIRLNEELKVDEESECSARLPPPVSGILCVRACVVCT
-Example Ensemble Genes:
-#name	seq
-ENST00000004921	MKGLAAALLVLVCTMALCSCAQVGTNKELCCLVYTSWQIPQKFIVDYSETSPQCPKPGVILLTKRGRQICADPNKKWVQKYISDLKLNA
-ENST00000005180	MMGLSLASAVLLASLLSLHLGTATRGSDISKTCCFQYSHKPLPWTWVRSYEFTSNSCSQRAVIFTTKRGKKVCTHPRKKWVQKYISLLKTPKQL
-
-6.) Uniprot ID-mapping file (optional, but recommended)
+
+    Example UCSC Genes:
+    #name	seq
+    uc010nxq.1	    MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCLPSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH
+    uc001adj.1	MQRWIMEKTAEHFQEAMEESKTHFRAVDPDGDGHVSWDEYKVKFLASKGHSEKEVADAIRLNEELKVDEESECSARLPPPVSGILCVRACVVCT
+    Example Ensemble Genes:
+    #name	seq
+    ENST00000004921	MKGLAAALLVLVCTMALCSCAQVGTNKELCCLVYTSWQIPQKFIVDYSETSPQCPKPGVILLTKRGRQICADPNKKWVQKYISDLKLNA
+    ENST00000005180	MMGLSLASAVLLASLLSLHLGTATRGSDISKTCCFQYSHKPLPWTWVRSYEFTSNSCSQRAVIFTTKRGKKVCTHPRKKWVQKYISLLKTPKQL
+

+
+Uniprot ID-mapping file (optional, but recommended)
+---------------------------------------------------
 For the id mapping only the Uniprot ID-mapping file with tab-separation is supported yet. It can be downloaded from the Uniprot FTP for several species
 (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/).
 
 E.g. for a Human ID-mapping file, browse the FTP directory, change to the "by organism" directory and download the corresponding tab-file (like "HUMAN*.tab").
 For an example open "examples\Uniprot_idmapping.tab" with a text editor.
 
 
-5.) Proteome fasta file (optional)
-The mapping might be supported by a proteome fasta, e.g. with those proteins used for the peptide identifications.
-In general, a recommanded source for proteoms is the Uniprot database, e.g. their FTP (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/).
-
-E.g. for the human PSMs example you can just download the human proteome in fasta format from the Uniprot FTP server.
-
-The data in the file should look like this:
->sp|A0A183|LCE6A_HUMAN Late cornified envelope protein 6A OS=Homo sapiens GN=LCE6A PE=2 SV=1
-MSQQKQQSWKPPNVPKCSPPQRSNPCLAPYSTPCGAPHSEGCHSSSQRPEVQKPRRARQK
-LRCLSRGTTYHCKEEECEGD
->tr|A0A4R5|A0A4R5_HUMAN Keratin 19 (Fragment) OS=Homo sapiens GN=keratin 19 PE=2 SV=1
-TIENARIVLQINNAQLAADDF
-
-
-6.) Reference Chromosomes (for GeneControl)
-If you are going to use the GeneControl, you will need a set of reference chromosomes (resp. scaffolds) covering all the genes in the annotation file.
-You have to provide a fasta file (*.fa!) for each chromosome in one folder, whereby the file names must correspond to the chromomosome names in the annotations (e.g. chr1.fa, chrX.fa, chrIV.fa, etc.) .
-Again, UCSC is a recommanded source for the data (http://hgdownload.cse.ucsc.edu/downloads.html).
-
-E.g. to get a human chromosome reference set, choose "human" from the vertebrates at the suggested download site, continue with "Full data set" and download the "chromFa.tar.gz" file from the button of the page.
-Extract the archive to folder of your choice which you can indicated in the GeneControl later.
+Proteome fasta file (optional)
+------------------------------
+The mapping might be supported by a proteome fasta, e.g. with those proteins used for the peptide identifications. In general, a recommanded source for proteoms is the Uniprot database, e.g. their FTP (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/). For the human PSMs example you can just download the human proteome in fasta format from the Uniprot FTP server.
+
+The data in the file should look like this:
+
+    >sp|A0A183|LCE6A_HUMAN Late cornified envelope protein 6A OS=Homo sapiens GN=LCE6A PE=2 SV=1
+    MSQQKQQSWKPPNVPKCSPPQRSNPCLAPYSTPCGAPHSEGCHSSSQRPEVQKPRRARQK
+    LRCLSRGTTYHCKEEECEGD
+    >tr|A0A4R5|A0A4R5_HUMAN Keratin 19 (Fragment) OS=Homo sapiens GN=keratin 19 PE=2 SV=1
+    TIENARIVLQINNAQLAADDF
+

+
+Reference Chromosomes (for GeneControl)
+---------------------------------------
+If you are going to use the GeneControl, you will need a set of reference chromosomes (resp. scaffolds) covering all the genes in the annotation file. You have to provide a fasta file (*.fa!) for each chromosome in one folder, whereby the file names must correspond to the chromosome names in the annotations (e.g. chr1.fa, chrX.fa, chrIV.fa, etc.).
+Again, UCSC is a good source for the data (http://hgdownload.cse.ucsc.edu/downloads.html).
+
+E.g. to get a human chromosome reference set, choose "human" from the vertebrates at the suggested download site, continue with "Full data set" and download the "chromFa.tar.gz" file from the button of the page. Extract the archive to folder of your choice which you can indicated in the GeneControl later.

WikiPage Data Formats modified by Mathias Kuhring

Mathias Kuhring — Fri, 16 Mar 2012 18:22:54 -0000

For the mapping of peptide spectrum matches (PSMs) to the genome you will need a file with your PSMs of interest and some files containing information about gene locations and protein-gene connections, as described below. In generel, you will find example files of some data descript here in the "examples" folder coming with the tool (except mzIdentML and chromosome files). Please note, they are just excerpts, thus not suitable for real usage. Peptide spectrum matches ------------------------ The PSMs of interest should be provided in the **mzIdentML** format (*.mzid) which is a XML based standard specific for peptide and protein identifications from mass spectra. The integrity of the input file will be checked with a XML schema (currently: mzIdentML1.0.0.xsd). For more details about the format visit the webpage ot the HUPO Proteomics Standards Initiative (http://www.psidev.info/index.php?q=node/403). For your information, iPiG will import every "PeptideEvidence" element from the "SpectrumIdentificationItem" elements pooled with necessary information from the referenced peptides ("Peptide_ref" attribute) and proteins ("DBSequence_Ref" attribute) which are the peptide sequences and modification as well as protein accessions and descriptions. As an **alternative** to the mzIdentML format, iPiG can import a simple tab-separated text file. E.g. you can extract such files from Mascot Search Results exported as CSV files by removing all header lines except the column titles and removing those columns which are not included in the example below. Please note, the names and order of the remaing columns are importened, since these files are verified by the header. In addition, sometimes it seems to be necessary to add some columns manually, e.g. "pep_isunique" The data in the text file should look like this: prot_acc | prot_desc | pep_query | pep_isunique | pep_exp_z | pep_score | pep_seq | pep_var_mod | pep_var_mod_pos prot_acc prot_desc pep_query pep_isunique pep_exp_z pep_score pep_seq pep_var_mod pep_var_mod_pos CPSM_HUMAN Carbamoyl-phosphate synthase ammonia, mitochondrial OS=Homo sapiens GN=CPS1 PE=1 SV=2 99 1 2 5.36 ASRSFPFVSK FAS_HUMAN Fatty acid synthase OS=Homo sapiens GN=FASN PE=1 SV=3 149 1 2 60.67 VGDPQELNGITR 2.) Gene Annotations As gene annotations UCSC and Ensembl genes in the UCSC table format (tab-separated) are supported yet, thus the UCSC Table Browser is recommanded as source (http://genome.ucsc.edu/cgi-bin/hgTables?command=start). E.g. if you like map peptide spectrum matches (PSMs) obtained from a human sample, go to the Table Browser and use the following settings: clade: "Mammal", genome: "Human", assembly: "Feb. 2009 (GRCh37/hg19)" (resp. the latest), group: "Genes and Gene Prediction Tracks", track: "UCSC Genes" or "Ensembl Genes" table: "knownGene" resp. "ensGene", region: "genome", output format: "all fields from selected table" Indicate a file name (*.txt) in the field "output file" and download the file via the "get output" button. The data in the file should look like this: Example UCSC Genes: #name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds proteinID alignID uc009vjk.2 chr1 + 322036 326938 324342 325605 3 322036,324287,324438, 322228,324345,326938, C9J4L2 uc009vjk.2 uc001aau.3 chr1 + 323891 328581 324342 325605 3 323891,324287,324438, 324060,324345,328581, C9J4L2 uc001aau.3 Example Ensemble Genes: #bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames 9 ENST00000472741 chr1 - 1026425 1051467 1051467 1051467 3 1026425,1027370,1051439, 1026945,1027483,1051467, 0 ENSG00000131591 none none -1,-1,-1, 34 ENST00000478275 chr1 - 212859759 212872097 212872097 212872097 2 212859759,212870302, 212860321,212872097, 0 ENSG00000123685 none none -1,-1, 3.) Amino Acid Sequences The amino acid sequences have to correspond to the gene annotations, therefore they have to be in the UCSC table format (tab-separated) as well. Oviously, the UCSC Table Browser is a recommanded source for this data, too (http://genome.ucsc.edu/cgi-bin/hgTables?command=start). E.g. following the example with human PSMs, the parameters are mainly the same, except one field: table: "knownGenePep" resp. "ensPep" Just save the data like descripted above. The data in the file should look like this: Example UCSC Genes: #name seq uc010nxq.1 MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCLPSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH uc001adj.1 MQRWIMEKTAEHFQEAMEESKTHFRAVDPDGDGHVSWDEYKVKFLASKGHSEKEVADAIRLNEELKVDEESECSARLPPPVSGILCVRACVVCT Example Ensemble Genes: #name seq ENST00000004921 MKGLAAALLVLVCTMALCSCAQVGTNKELCCLVYTSWQIPQKFIVDYSETSPQCPKPGVILLTKRGRQICADPNKKWVQKYISDLKLNA ENST00000005180 MMGLSLASAVLLASLLSLHLGTATRGSDISKTCCFQYSHKPLPWTWVRSYEFTSNSCSQRAVIFTTKRGKKVCTHPRKKWVQKYISLLKTPKQL 6.) Uniprot ID-mapping file (optional, but recommended) For the id mapping only the Uniprot ID-mapping file with tab-separation is supported yet. It can be downloaded from the Uniprot FTP for several species (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/). E.g. for a Human ID-mapping file, browse the FTP directory, change to the "by organism" directory and download the corresponding tab-file (like "HUMAN*.tab"). For an example open "examples\Uniprot_idmapping.tab" with a text editor. 5.) Proteome fasta file (optional) The mapping might be supported by a proteome fasta, e.g. with those proteins used for the peptide identifications. In general, a recommanded source for proteoms is the Uniprot database, e.g. their FTP (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/). E.g. for the human PSMs example you can just download the human proteome in fasta format from the Uniprot FTP server. The data in the file should look like this: >sp|A0A183|LCE6A_HUMAN Late cornified envelope protein 6A OS=Homo sapiens GN=LCE6A PE=2 SV=1 MSQQKQQSWKPPNVPKCSPPQRSNPCLAPYSTPCGAPHSEGCHSSSQRPEVQKPRRARQK LRCLSRGTTYHCKEEECEGD >tr|A0A4R5|A0A4R5_HUMAN Keratin 19 (Fragment) OS=Homo sapiens GN=keratin 19 PE=2 SV=1 TIENARIVLQINNAQLAADDF 6.) Reference Chromosomes (for GeneControl) If you are going to use the GeneControl, you will need a set of reference chromosomes (resp. scaffolds) covering all the genes in the annotation file. You have to provide a fasta file (*.fa!) for each chromosome in one folder, whereby the file names must correspond to the chromomosome names in the annotations (e.g. chr1.fa, chrX.fa, chrIV.fa, etc.) . Again, UCSC is a recommanded source for the data (http://hgdownload.cse.ucsc.edu/downloads.html). E.g. to get a human chromosome reference set, choose "human" from the vertebrates at the suggested download site, continue with "Full data set" and download the "chromFa.tar.gz" file from the button of the page. Extract the archive to folder of your choice which you can indicated in the GeneControl later.