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General Category >> Feature Requests >> enhanced primer search https://forum.ugene.net/forum/YaBB.pl?num=1453895718 Message started by Nex on Jan 27th, 2016 at 6:55pm |
Title: enhanced primer search Post by Nex on Jan 27th, 2016 at 6:55pm
Hello, thanks (as always) for the hard work on Ugene, and for carrying on!
I would like to make a suggestion for an especial case in searches: when you search for primer binding sites in a sequence. Currently, a search can be relaxed down by setting a % matching. However, in the case of primers this gives information that can be filtered. Polymerisation in PCR starts at the 3' end of a primer, so matching the 3' is critical whilst matching the 5' end can be irrelevant (e.g. in a long sequence, the 5' end can be just hanging free, but the primer attaches to the sequence by the 3' end and polymerisation starts). The matching algorithm can be as complicated as you wish, but I think that in order of preference: - I would give more weigh to the 3' end 1to5 > 6to10 > 10to15 bases, and would add a tick to consider irrelevant the 20+ bases towards the 5' end, or when starting from the 3' end a threshold Tm is reached. - G and C at the 3' end have more weigh than A and T (due to melting temperature) - melting temperature calculations can be made, to apply thresholds (e.g. discard melting temperatures below 45 degrees). - a combination of melting temperature and matching (number of bases matched, giving more weight to bases clustered closer to the 3' end) can be scored, so the primers are given in a meaningful order (primers with more matching bases at the 3' end can start polymerisation more likely. But e.g. a primer with no matches in the first 1 bases at the 3' is will not polymerise unless reaction conditions are relaxed, and a primer with 2 unmatched bases at the 3' end will be extremely unlikely to polymerise in standard conditions). - a results window can be provided, visually showing the matching of the primers like an alignment, so the user can visually assess (matching algorithms can be initially simpler then) and select primer binding sites to be added to the project. - It would be nice to show 5' unmatched binding with hanging ends like Snapgene does. Hope the suggestions help, any comments appreciated. All the best! |
Title: Re: enhanced primer search Post by ClayAnderson2 on Sep 19th, 2016 at 6:10pm
thank you
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Title: Re: enhanced primer search Post by Doucan on Dec 19th, 2016 at 3:34pm
Good suggestion.
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Title: Re: enhanced primer search Post by Jamesym on Apr 13th, 2019 at 3:06am Nex wrote on Jan 27th, 2016 at 6:55pm:
Thank you so much it is very informative and i am glad to be here and get valuable solutions |
Title: Re: enhanced primer search Post by MichaelGoins on Oct 16th, 2020 at 5:55pm wrote on May 7th, 2439 at 11:34am:
Could you please suggest me or guide me what he say ? |
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