https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/Recent changes to GenoSuiteenWed, 15 Oct 2014 03:31:06 -0000https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v22 +++ v23 @@ -1,8 +1,8 @@ **GenoSuite** is an automated pipeline for proteogenomic analysis from mass spectrometry proteomics data using four open source peptide identification algorithms. By applying proteomic search by multiple algorithms, GenoSuite provides better coverage of proteome at fixed FDR. It automatically classifies identified peptides into categories of already annotated genes or originating from an genomic region, unknown for translation. GenoSuite can be used for genome annotation/re-annotation projects provided tandem mass spectrometry data and genome sequence are available. Search parameters can be customized and and any combination of algorithm can be chosen for search. The four algorithms configured are **OMSSA**, **X!Tandem**, **InsPecT** and **MassWiz**. -New version ***GenoSuite_v_2.0.3*** released. This new version allows to add a contaminant protein list to the genome translated search database. Bugs related to PSM XML generation and visualization are also fixed. +New version ***GenoSuite_v_2.0.3*** released. This new version allows to add a contaminant protein list to the genome translated search database. Bugs related to PSM XML generation and visualization are also fixed. -[[download_button]] +[[download_button]] ***GenoSuite2*** is an updated version where following major changes are made to make is more applicable and accurate. </pre> </div>Dhirendra KumarWed, 15 Oct 2014 03:31:06 -0000https://sourceforge.net99ac0d8c139560846005e18083b8403575a08158https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v21 +++ v22 @@ -1,8 +1,8 @@ **GenoSuite** is an automated pipeline for proteogenomic analysis from mass spectrometry proteomics data using four open source peptide identification algorithms. By applying proteomic search by multiple algorithms, GenoSuite provides better coverage of proteome at fixed FDR. It automatically classifies identified peptides into categories of already annotated genes or originating from an genomic region, unknown for translation. GenoSuite can be used for genome annotation/re-annotation projects provided tandem mass spectrometry data and genome sequence are available. Search parameters can be customized and and any combination of algorithm can be chosen for search. The four algorithms configured are **OMSSA**, **X!Tandem**, **InsPecT** and **MassWiz**. New version ***GenoSuite_v_2.0.3*** released. This new version allows to add a contaminant protein list to the genome translated search database. Bugs related to PSM XML generation and visualization are also fixed. + [[download_button]] - ***GenoSuite2*** is an updated version where following major changes are made to make is more applicable and accurate. @@ -30,4 +30,4 @@ If GenoSuite is helpful to your research, please consider citing following reference. -***Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using Genosuite , an automated multi-algorithmic pipeline. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Mol Cell Proteomics. 2013 Jul 23.*** +***Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using Genosuite, an automated multi-algorithmic pipeline. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Mol Cell Proteomics. 2013 Jul 23.*** </pre> </div>Dhirendra KumarWed, 15 Oct 2014 03:29:22 -0000https://sourceforge.net41620ccc073840aeb5a64bf6960bae65b14e6a41https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v20 +++ v21 @@ -2,6 +2,8 @@ New version ***GenoSuite_v_2.0.3*** released. This new version allows to add a contaminant protein list to the genome translated search database. Bugs related to PSM XML generation and visualization are also fixed. [[download_button]] + + ***GenoSuite2*** is an updated version where following major changes are made to make is more applicable and accurate. </pre> </div>Dhirendra KumarWed, 15 Oct 2014 03:27:26 -0000https://sourceforge.netabaaf48376807e18a0f4981d75bf82582fdfe632https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v19 +++ v20 @@ -1,6 +1,7 @@ **GenoSuite** is an automated pipeline for proteogenomic analysis from mass spectrometry proteomics data using four open source peptide identification algorithms. By applying proteomic search by multiple algorithms, GenoSuite provides better coverage of proteome at fixed FDR. It automatically classifies identified peptides into categories of already annotated genes or originating from an genomic region, unknown for translation. GenoSuite can be used for genome annotation/re-annotation projects provided tandem mass spectrometry data and genome sequence are available. Search parameters can be customized and and any combination of algorithm can be chosen for search. The four algorithms configured are **OMSSA**, **X!Tandem**, **InsPecT** and **MassWiz**. New version ***GenoSuite_v_2.0.3*** released. This new version allows to add a contaminant protein list to the genome translated search database. Bugs related to PSM XML generation and visualization are also fixed. +[[download_button]] ***GenoSuite2*** is an updated version where following major changes are made to make is more applicable and accurate. </pre> </div>Dhirendra KumarWed, 15 Oct 2014 03:27:05 -0000https://sourceforge.netcdd82307bc34b1b4aa5d54e120794c7a64f5827chttps://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v18 +++ v19 @@ -19,6 +19,9 @@ https://sourceforge.net/p/proteogenomic/wiki/Proteogenomic%20Re-annotation%20of%20Shigellla%20flexneri/ +***Methylobacterium extorquens*** **AM1** + +https://sourceforge.net/p/proteogenomic/wiki/Methylobacterium%20extorquens%20AM1/ **Citing GenoSuite** </pre> </div>Dhirendra KumarWed, 30 Apr 2014 01:28:30 -0000https://sourceforge.net34f1896ac58de77d9145098160a900f0947ea8f6https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v17 +++ v18 @@ -20,8 +20,8 @@ https://sourceforge.net/p/proteogenomic/wiki/Proteogenomic%20Re-annotation%20of%20Shigellla%20flexneri/ -Citing GenoSuite +**Citing GenoSuite** If GenoSuite is helpful to your research, please consider citing following reference. -Proteogenomic analysis of ***Bradyrhizobium japonicum*** USDA110 using ***Genosuite*** , an automated multi-algorithmic pipeline. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Mol Cell Proteomics. 2013 Jul 23. +***Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using Genosuite , an automated multi-algorithmic pipeline. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Mol Cell Proteomics. 2013 Jul 23.*** </pre> </div>Dhirendra KumarFri, 16 Aug 2013 06:35:21 -0000https://sourceforge.netee8342c511b86b99f76f4bd1c3a65bcf38a0c249https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v16 +++ v17 @@ -24,5 +24,4 @@ If GenoSuite is helpful to your research, please consider citing following reference. -Proteogenomic analysis of ***Bradyrhizobium japonicum*** USDA110 using ***Genosuite*** , an automated -multi-algorithmic pipeline. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Mol Cell Proteomics. 2013 Jul 23. +Proteogenomic analysis of ***Bradyrhizobium japonicum*** USDA110 using ***Genosuite*** , an automated multi-algorithmic pipeline. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Mol Cell Proteomics. 2013 Jul 23. </pre> </div>Dhirendra KumarWed, 14 Aug 2013 20:52:52 -0000https://sourceforge.net64d50e614ad81429d53618b3c12271fa5737ed50https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v15 +++ v16 @@ -18,3 +18,11 @@ ***Shigella flexneri*** **2a str. 2457T** https://sourceforge.net/p/proteogenomic/wiki/Proteogenomic%20Re-annotation%20of%20Shigellla%20flexneri/ + + +Citing GenoSuite + +If GenoSuite is helpful to your research, please consider citing following reference. + +Proteogenomic analysis of ***Bradyrhizobium japonicum*** USDA110 using ***Genosuite*** , an automated +multi-algorithmic pipeline. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Mol Cell Proteomics. 2013 Jul 23. </pre> </div>Dhirendra KumarWed, 14 Aug 2013 20:51:45 -0000https://sourceforge.net9e7e92322762d773fd4b2b271a17dcdde83260c0https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v14 +++ v15 @@ -2,7 +2,7 @@ New version ***GenoSuite_v_2.0.3*** released. This new version allows to add a contaminant protein list to the genome translated search database. Bugs related to PSM XML generation and visualization are also fixed. -***GenoSuite2*** is an updated version where following major changes are performed to make is more applicable and accurate. +***GenoSuite2*** is an updated version where following major changes are made to make is more applicable and accurate. (1) **Combined FDRScore** based strategy has been implemented to integrate results from four algorithms at the level of peptide spectrum matches(PSMs). This approach was originally proposed and implemented on OMSSA, Mascot and X!Tandem by Jones AR et al.(Proteomics 2009). In GenoSuite we have extended this approach to **InsPecT** and **MassWiz**. This allows us to estimate and control false discovery rates after the integration of results from different algorithms. </pre> </div>Dhirendra KumarFri, 31 May 2013 11:37:03 -0000https://sourceforge.net8deac2d86299287a6e1b9b22585ec006872e9f19https://sourceforge.net/p/proteogenomic/wiki/GenoSuite/<div class="markdown_content"><pre>--- v13 +++ v14 @@ -1,4 +1,6 @@ **GenoSuite** is an automated pipeline for proteogenomic analysis from mass spectrometry proteomics data using four open source peptide identification algorithms. By applying proteomic search by multiple algorithms, GenoSuite provides better coverage of proteome at fixed FDR. It automatically classifies identified peptides into categories of already annotated genes or originating from an genomic region, unknown for translation. GenoSuite can be used for genome annotation/re-annotation projects provided tandem mass spectrometry data and genome sequence are available. Search parameters can be customized and and any combination of algorithm can be chosen for search. The four algorithms configured are **OMSSA**, **X!Tandem**, **InsPecT** and **MassWiz**. + +New version ***GenoSuite_v_2.0.3*** released. This new version allows to add a contaminant protein list to the genome translated search database. Bugs related to PSM XML generation and visualization are also fixed. ***GenoSuite2*** is an updated version where following major changes are performed to make is more applicable and accurate. </pre> </div>Dhirendra KumarFri, 31 May 2013 11:36:15 -0000https://sourceforge.net9abc04d97e082bfe62094c5fae03bb957c3329ce