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Home modified by Filip Wierzbicki

Filip Wierzbicki — Wed, 01 Dec 2021 10:38:27 -0000

--- v23
+++ v24
@@ -2,7 +2,7 @@
 # Introduction
 Welcome to Manna, a novel tool to align multiple sequences of annotations (e.g. RepeatMasker annotations of piRNA clusters).
 # Genome assemblies
-We additionally generated long-read assemblies of two *D. simulans* lines: https://sourceforge.net/projects/manna/files/assemblies/ 
+We generated long-read assemblies of two *D. simulans* lines (SZ232 and SZ45): https://sourceforge.net/projects/manna/files/assemblies/

 (for completeness, other assemblies used in this work:  https://sourceforge.net/projects/manna/files/assemblies/previously_published-assemblies/)
 # Manual

Home modified by Filip Wierzbicki

Filip Wierzbicki — Wed, 01 Dec 2021 10:26:06 -0000

--- v22
+++ v23
@@ -3,6 +3,8 @@
 Welcome to Manna, a novel tool to align multiple sequences of annotations (e.g. RepeatMasker annotations of piRNA clusters).
 # Genome assemblies
 We additionally generated long-read assemblies of two *D. simulans* lines: https://sourceforge.net/projects/manna/files/assemblies/ 
+
+(for completeness, other assemblies used in this work:  https://sourceforge.net/projects/manna/files/assemblies/previously_published-assemblies/)
 # Manual
 Please consult the [Manual] for explanation of the core script.
 # Walkthrough

Home modified by Robert Kofler

Robert Kofler — Tue, 30 Nov 2021 15:23:30 -0000

--- v21
+++ v22
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 Finally the (official) Manna song https://www.youtube.com/watch?v=8N_tupPBtWQ&ab_channel=VeselinTrayanov

 #piRNAclusterComparison
-Complementarily, we can visualize piRNA cluster comparisons based on their nucleotide sequence and corresponding TE annotations based on a modified version of easyfig. 
+Complementarily to Manna, we can also visualize the comparision of piRNA cluster with EasyFig, which uses the similarity between the aligned sequences and the TE annoations. 
 Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011 Apr 1;27(7):1009-10. doi: 10.1093/bioinformatics/btr039. Epub 2011 Jan 28. PMID: 21278367; PMCID: PMC3065679.
-A walkthrough with cluster 38C of 3 *D. melanogaster* assemblies can be found here [piRNAclusterComparison-walkthrough].
-Although easyfig supports comparisons of multiple sequences, the option can solely mantain feature labels (i.e. TE names) of the first and last assembly. To prevent loss of feature labels of other assemblies, we combine pairwise comparisons in this pipeline. 
-Additionally, we modified the originial easyfig script to write labels in a monospaced font (consolas) and to set the blastn similiarity to a fixed range between 70%-100% to allow for comparisons of individually generated plots. 
-In this way we can visualize comparisons of clusters from multiple assemblies  (currently, up to 9 assemblies). 
+
+A walkthrough for this visualization with cluster 38C for three *D. melanogaster* strains can be found here [piRNAclusterComparison-walkthrough].
+Although EasyFig supports comparisons of multiple sequences, this feature can solely display the feature labels (e.g. the TE names) of the first and the last assembly. To prevent loss of feature labels for the intermediate  assemblies, we perform pairwise comparisions and then combine them. 
+Additionally, we modified the originial EasyFig script to write labels in a monospaced font (consolas) and to set the blastn similiarity to a fixed range between 70%-100% which enables us to compare the individually generated plots. 
+We are thus able  to visualize comparisons of clusters from multiple assemblies  (currently, up to 9 assemblies). 
 Note that currently several parameters are hardcoded in this pipeline (e.g. color *D. melanogaster*  TEs by orders or a miminium blastn similarity block of 3 kb).

 [[members limit=20]]

Home modified by Robert Kofler

Robert Kofler — Tue, 30 Nov 2021 15:05:31 -0000

--- v20
+++ v21
@@ -2,11 +2,11 @@
 # Introduction
 Welcome to Manna, a novel tool to align multiple sequences of annotations (e.g. RepeatMasker annotations of piRNA clusters).
 # Genome assemblies
-We additionally generated long-read assemblies of two * D. simulans* lines: https://sourceforge.net/projects/manna/files/assemblies/ 
+We additionally generated long-read assemblies of two *D. simulans* lines: https://sourceforge.net/projects/manna/files/assemblies/ 
 # Manual
 Please consult the [Manual] for explanation of the core script.
 # Walkthrough
-For the piRNA cluster 42AB from 5 *D. melanogaster* lines a [Walkthrough] is available.
+A [Walkthrough] is available using piRNA cluster 42AB from 5 *D. melanogaster* lines 
 # Toy examples
 Several evolutionary scenarios are shown in [Toy examples].
 # Validation

Home modified by Filip Wierzbicki

Filip Wierzbicki — Fri, 26 Nov 2021 08:36:18 -0000

--- v19
+++ v20
@@ -1,6 +1,8 @@
 [TOC]
 # Introduction
 Welcome to Manna, a novel tool to align multiple sequences of annotations (e.g. RepeatMasker annotations of piRNA clusters).
+# Genome assemblies
+We additionally generated long-read assemblies of two * D. simulans* lines: https://sourceforge.net/projects/manna/files/assemblies/ 
 # Manual
 Please consult the [Manual] for explanation of the core script.
 # Walkthrough

Home modified by Filip Wierzbicki

Filip Wierzbicki — Thu, 25 Nov 2021 12:17:33 -0000

--- v18
+++ v19
@@ -1,6 +1,6 @@
 [TOC]
 # Introduction
-Welcome to Manna, a novel tool to align multiple sequence of annotations (e.g. RepeatMasker annotations of piRNA clusters).
+Welcome to Manna, a novel tool to align multiple sequences of annotations (e.g. RepeatMasker annotations of piRNA clusters).
 # Manual
 Please consult the [Manual] for explanation of the core script.
 # Walkthrough

Home modified by Filip Wierzbicki

Filip Wierzbicki — Thu, 25 Nov 2021 12:16:39 -0000

--- v17
+++ v18
@@ -1,8 +1,8 @@
 [TOC]
 # Introduction
-
+Welcome to Manna, a novel tool to align multiple sequence of annotations (e.g. RepeatMasker annotations of piRNA clusters).
 # Manual
-
+Please consult the [Manual] for explanation of the core script.
 # Walkthrough
 For the piRNA cluster 42AB from 5 *D. melanogaster* lines a [Walkthrough] is available.
 # Toy examples

Home modified by Filip Wierzbicki

Filip Wierzbicki — Thu, 05 Aug 2021 11:01:52 -0000

--- v16
+++ v17
@@ -23,7 +23,7 @@
 Although easyfig supports comparisons of multiple sequences, the option can solely mantain feature labels (i.e. TE names) of the first and last assembly. To prevent loss of feature labels of other assemblies, we combine pairwise comparisons in this pipeline. 
 Additionally, we modified the originial easyfig script to write labels in a monospaced font (consolas) and to set the blastn similiarity to a fixed range between 70%-100% to allow for comparisons of individually generated plots. 
 In this way we can visualize comparisons of clusters from multiple assemblies  (currently, up to 9 assemblies). 
-Note that currently several parameters are hardcoded in this pipeline (e.g. color *D. melanogaster*  TEs by orders or a miminium blastn similiarity block of 3 kb).
+Note that currently several parameters are hardcoded in this pipeline (e.g. color *D. melanogaster*  TEs by orders or a miminium blastn similarity block of 3 kb).

 [[members limit=20]]
 [[download_button]]

Home modified by Filip Wierzbicki

Filip Wierzbicki — Thu, 05 Aug 2021 11:01:03 -0000

--- v15
+++ v16
@@ -23,7 +23,7 @@
 Although easyfig supports comparisons of multiple sequences, the option can solely mantain feature labels (i.e. TE names) of the first and last assembly. To prevent loss of feature labels of other assemblies, we combine pairwise comparisons in this pipeline. 
 Additionally, we modified the originial easyfig script to write labels in a monospaced font (consolas) and to set the blastn similiarity to a fixed range between 70%-100% to allow for comparisons of individually generated plots. 
 In this way we can visualize comparisons of clusters from multiple assemblies  (currently, up to 9 assemblies). 
-Note that currently several parameters are hardcoded in this pipeline (e.g. color TEs by the 3 orders (TIRs,non-LTRs, LTRs) or a miminium blastn similiarity block of 3 kb).
+Note that currently several parameters are hardcoded in this pipeline (e.g. color *D. melanogaster*  TEs by orders or a miminium blastn similiarity block of 3 kb).

 [[members limit=20]]
 [[download_button]]

Home modified by Filip Wierzbicki

Filip Wierzbicki — Thu, 05 Aug 2021 10:59:31 -0000

--- v14
+++ v15
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 # The (official) Manna song
 Finally the (official) Manna song https://www.youtube.com/watch?v=8N_tupPBtWQ&ab_channel=VeselinTrayanov

-Welcome to your wiki!
-
-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
-
-The wiki uses [Markdown](/p/manna/wiki/markdown_syntax/) syntax.
+#piRNAclusterComparison
+Complementarily, we can visualize piRNA cluster comparisons based on their nucleotide sequence and corresponding TE annotations based on a modified version of easyfig. 
+Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011 Apr 1;27(7):1009-10. doi: 10.1093/bioinformatics/btr039. Epub 2011 Jan 28. PMID: 21278367; PMCID: PMC3065679.
+A walkthrough with cluster 38C of 3 *D. melanogaster* assemblies can be found here [piRNAclusterComparison-walkthrough].
+Although easyfig supports comparisons of multiple sequences, the option can solely mantain feature labels (i.e. TE names) of the first and last assembly. To prevent loss of feature labels of other assemblies, we combine pairwise comparisons in this pipeline. 
+Additionally, we modified the originial easyfig script to write labels in a monospaced font (consolas) and to set the blastn similiarity to a fixed range between 70%-100% to allow for comparisons of individually generated plots. 
+In this way we can visualize comparisons of clusters from multiple assemblies  (currently, up to 9 assemblies). 
+Note that currently several parameters are hardcoded in this pipeline (e.g. color TEs by the 3 orders (TIRs,non-LTRs, LTRs) or a miminium blastn similiarity block of 3 kb).

 [[members limit=20]]
 [[download_button]]