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Such unique know-how is contained in the fitment list available in the download section of this web-site and in the chain selection tool here below. This chart is only to be used as a general guide. For actual chain fitment, please refer to the Fitment List. A wide range of tools, including spare parts, to install and maintain your chains. A correct maintenance allows your chain to last longer and to obtain the best performance out of it.
Search your Chain. The contents of this page are from Angie 's mental model of chains and nets and represent opinions which may be outdated or plain old incorrect. The source code, and the results that we get by running these programs on real data, are the ultimate source of truth about chains and nets.
Please keep in mind that the outputs of any alignment algorithm are not the final Truth about homology between sequences. The scoring system and other parameters of any alignment algorithm are designed to produce high scores for similarities that would likely result from some model of nucleotide-level evolution; tweaking a parameter can change the results significantly. The quality and completeness of the reference assemblies also affect alignment results.
That said, chains and nets are powerful constructs for identifying similarities over very large regions of the genome, and inferring chromosomal rearrangements that may have occurred as the two sequences diverged from a common ancestral sequence. In chain and net lingo, the target is the reference genome sequence and the query is some other genome sequence.
For example, if you are viewing Human-Mouse alignments in the Human genome browser, human is the target and mouse is the query. A gapless block is a base-for-base alignment between part of the target and part of the query, possibly including mismatching bases. It has the same length in bases on the target and the query. This is the output of the most primitive alignment algorithms. A gap is a link between two gapless blocks, indicating that the target or the query has sequence that should be skipped over in order to make the best-scoring alignment.
In other words, the scoring penalty for skipping over one or more bases is less than the penalty for continuing to align the sequences without skipping. A single-sided gap is a gap in which sequence in either target or query must be skipped over. A plausible explanation for needing to skip over a base in the target while not skipping a base in the query is that either the target has an inserted base or the query has a deleted base.
Many alignment tools produce alignments with single-sided gaps between gapless blocks. A double-sided gap skips over sequence in both target and query because the sum of penalties for mismatching bases exceeds the penalty for extending a gap across them. This is possible only when the penalty for extending a gap is less than the penalty for creating a new gap and less than the penalty for a mismatch, and when the alignment algorithm is capable of considering double-sided gaps.
A chain is a sequence of non-overlapping gapless blocks, with single- or double-sided gaps between blocks. Within a chain, target and query coords are monotonically non-decreasing i. Chains are constructed by the axtChain program which finds pairwise alignments with the same target and query sequence, on the same strand, that can be merged if overlapping and joined into one longer alignment with a higher score under an affine gap-scoring system progressively decreasing penalties for longer gaps.
A net is a hierarchical collection of chains, with the highest-scoring non-overlapping chains on top, and their gaps filled in where possible by lower-scoring chains, which in turn may have gaps filled in by lower-level chains and so on. Chains and nets are Jim Kent 's brainchild, building on joint work with blastz author Scott Schwartz.
The original publication describing chains and net, Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes Kent et al.
Branches Tags. Could not load branches. Could not load tags. Latest commit. Git stats 43 commits. Failed to load latest commit information. View code. NET Spice up your enumerables with extra method chains. About Spice up your enumerables with extra method chains. Topics linq functional csharp netcore fluent-api.
Releases No releases published. Packages 0 No packages published. You signed in with another tab or window. Reload to refresh your session. Also notice note on bottom of page about Editing the human trackDb. You can run the following two scripts instead of doing the "Full QA" below using the chainNetTrio script. Check that the values for chainMinScore and chainLinearGap output by the script match the values listed in the track description page, under "Methods, Chain track", for the relevant track in the Genome Browser.
NOTE : In the latest assemblies, blastz is no longer used for scoring matrices, instead lastz is used. Instead, use the findScores. Check that the values for the matrix output by the script match the values shown in the track description page, under "Methods, Chain track", for the relevant track in the Genome Browser.
In cases such as this where you're not sure what the output of getChainLines. If you run getChainLines. Make sure first that you are looking at the correct assembly. For instructions on how to do this, see Editing trackDb. Use the following only if you do not do the Quick QA above. You do not need to do both, as the Full QA steps i. Run the chainNetTrio.
The chainNetTrio. It is recommended that you create a separate directory to run this script in so you don't end up with the random output files in another directory. Mainly check that all the scripts tested ok and do a few manual checks that requested in these files. See Replacing old tables with new ones i.
Use the same steps listed in step 4 above under "Prior to QAing on hgwbeta". Note that you do not need to push the liftOver file as the RR and hgwbeta both have access to hgnfs1. Note that the destination paths on hgdownload will only be "htdocs", not "htdocs-hgdownload".
Be sure to request genome-euro drop along with mysqlrr. Once push is complete, check to see that your changes are now on the public downloads page.