<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38008?offset=530 https://bioinformaticsonline.com/bookmarks/view/27216/yass-genomic-similarity-search-tool Mon, 02 May 2016 09:26:00 -0500 https://bioinformaticsonline.com/bookmarks/view/27216/yass-genomic-similarity-search-tool <![CDATA[YASS :: genomic similarity search tool]]> YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to local alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step (as provided for example by iedera).

Main features of YASS are:

  • multiple, possibly overlapping seeds and a new hit criterion to ensure a good sensitivity/selectivity trade-off
  • transition-constrained spaced seeds to improve sensitivity (transition mutations are purine to purine [A<->G] or pyrimidine to pyrimidine [C<->T])
  • using different scoring schemes with bit-score and E-value evaluated according to the sequence background frequencies
  • parameterizable output filter for low complexity repeats
  • reporting of various alignment statistical parameters (mutation bias along triplets, transition/transversion)
  • post-processing step to group gapped alignments

Address of the bookmark: http://bioinfo.lifl.fr/yass/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/28809/kissplice Tue, 16 Aug 2016 08:34:19 -0500 https://bioinformaticsonline.com/bookmarks/view/28809/kissplice <![CDATA[KisSplice]]> KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.

KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely.

KisSplice comes as a workflow, with several possible post-treatments meant to facilitate the analysis of the results. The choice of the post-treatment depends on the availability of a reference genome/transcriptome and on the need to perform a differential analysis, as summarised in the following table.

Address of the bookmark: http://kissplice.prabi.fr/

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