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The advanced search mechanism allows for complex filtering of variants in the database by allowing the user to create a set of rules that determine if a variant entry is or is not allowed the result set.
To begin, add at least one condition with the "Add Condition" button in the bottom left of the modal window. This adds a set of fields which can be used to create a single rule applying to a specific column in the database. The options for the new rule are broken down as follows: 1) A joining boolean operator (not present on the first operator). 2) An optional negation field that takes the rest of the condition and inverts it. For example, if the current condition is "gene_info contains 'LOC'", then this would turn the condition into "gene_info does not contain 'LOC'". 3) A field drop-down which specifies which field the condition should apply to. 4) An operator for the condition; the available operators depend on the type of data stored in the column. This relates the selected column with the value entered into the text box on the right (5).
For example, take the gene_info field. This field allows 9 different operators: equals, 4 inequality operators, starts/ends with, and contains. In this case, the contains operator is helpful. If the string "LOC" is being searched in the gene_info field, the contains operator would yield positive matches with, for example, "LOC105378947:105378947" or "KAZN:23254|LOC107985467:107985467". If the starts_with operator was used, only the first example would match.
The equals operator is available for all data types and only yields direct matches, meaning that the contents of the column entries must match exactly (with no room for any characters, including whitespace, on either side of a value). The inequality operators use the same order as when sorting the columns, so 2 < 3, 0.2 < 0.3, and abc < abe < bce.
The joining boolean operators available are AND and OR. They behave as follows, using "True" and "False" as results of the actual comparison operators described above (so, for example, 1 = 1 is True and "hello" contains "a" is False). Note that the OR used in this case is inclusive as opposed to exclusive.
True AND True is True; True AND False is False; True OR True is True; True OR False is True; False AND/OR False is False.
In this way, multiple rules can be strung together into a query. When the query is built, an encoded version can be saved by pressing the "Save" button, which will clear and re-populate the search field with a machine-readable version of the query. The query can then be optionally combined with "quick filters" in the sidebar before being used to filter the variants.
For example to select exonic rare variants whose micro-homology starts with at least 3 exact matches, with at most 10 bp of non-homologous sequence and with at least one PAM with unique protospacer:
location equals exon AND topmed < 0.01 AND mh_1l >= 3
AND mh_dist <= 10 AND pam_uniq > 0
Total Matching Variants: many
Total Matching Guides: many
The MHcut Code and Software are being provided under a Limited Copyright License for Research Use by Non-Profit and Government Institutions (GNU GPLv3). The MHcut Code and Software are being provided as a service for research, educational, instructional and non-commercial purposes only.
“Code” means the MHcut source code made available in the GitHub repository at https://github.com/WoltjenLab/MHcut; and “Software” means the code made available as a web service by the Canadian Centre for Computational Genomics and the Center for iPS Cell Research and Application, Kyoto University, at https://mhcut-browser.genap.ca/.
By using the Software or downloading the Code accompanying this license, you are consenting to be bound by all the terms of this license listed below.
“Copyright 2019. Canadian Centre for Computational Genomics and the Center for iPS Cell Research and Application, Kyoto University. All Rights Reserved.”
This web tool is hosted by the Canadian Center for Computational Genomics and was developed by the Woltjen lab at the Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan in collaboration with the Bourque lab at the Department of Human Genetics, McGill University, Montreal, Canada.
For more information and to report bugs, please contact Knut Woltjen.