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bioinformatics_tools

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bioinformatics_tools [2022/05/01 20:12] – 134.190.232.106bioinformatics_tools [2022/08/21 10:35] (current) – 173.212.112.187
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   - HSDFinder: a BLAST-based strategy for identifying highly similar duplicated genes in eukaryotic genomes (2021)   - HSDFinder: a BLAST-based strategy for identifying highly similar duplicated genes in eukaryotic genomes (2021)
   - HSDatabase – Identification and functional annotation of highly similar duplicated genes in eukaryotic genomes(2022)   - HSDatabase – Identification and functional annotation of highly similar duplicated genes in eukaryotic genomes(2022)
-  - Comprehensive analysis of gene duplications in eukaryotic genomes unravelling the convergent adaptive and nonadaptive evolution (2022)+  - An overview of online resources for gene duplication detection within species: Mini review(2022) 
 +  - HSDicipher: A downstream anaylysis package of hsdfiner and hsdatabase(2023)
  
 So far, the first step via designing the HSDFinder tool has been reached after so many trails, the selected eukaryotic species have been collected into the HSDatabase. The comprehensive analysis is on the way. So far, the first step via designing the HSDFinder tool has been reached after so many trails, the selected eukaryotic species have been collected into the HSDatabase. The comprehensive analysis is on the way.
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-**How to analyze the data from HSDFinder?**+**How to analyze the data from HSDFinder?** HSDicipher https://github.com/zx0223winner/HSDicipher
  
 Although there is no golden rule to distinguish partial duplicates from more complete ones, it is believed that the relative complete duplicates turn to have at least less than 50% amino acid length difference and same number and function of conserved domain.  Although there is no golden rule to distinguish partial duplicates from more complete ones, it is believed that the relative complete duplicates turn to have at least less than 50% amino acid length difference and same number and function of conserved domain. 
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   * HSD_Categories.py is to calculate the gene copies within each group, i.e., 2-group is the HSD group only has two gene copies.   * HSD_Categories.py is to calculate the gene copies within each group, i.e., 2-group is the HSD group only has two gene copies.
   * HSD_add_on.py is to merge a series of combo thresholds based on the formula:E + (D + (C + (B +A)))   * HSD_add_on.py is to merge a series of combo thresholds based on the formula:E + (D + (C + (B +A)))
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      * A = 90%_100aa+(90%_70aa+(90%_50aa+(90%_30aa+90%_10aa)))      * A = 90%_100aa+(90%_70aa+(90%_50aa+(90%_30aa+90%_10aa)))
      * B = 80%_100aa+(80%_70aa+(80%_50aa+(80%_30aa+80%_10aa)))      * B = 80%_100aa+(80%_70aa+(80%_50aa+(80%_30aa+80%_10aa)))
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      * E = 50%_100aa+(50%_70aa+(50%_50aa+(50%_30aa+50%_10aa)))      * E = 50%_100aa+(50%_70aa+(50%_50aa+(50%_30aa+50%_10aa)))
  
-<Last updated by Xi Zhang on Oct 6th,2021> Upcoming+<Last updated by Xi Zhang on Oct 6th,2021> 
 +<Last updated by Xi Zhang on May 1st,2022>
bioinformatics_tools.1651446746.txt.gz · Last modified: by 134.190.232.106