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SyMAP - University of Arizona SyMAP (Synteny Mapping and Analysis Program) is a software package for detecting, displaying, and querying syntenic relationships between sequenced genomes It is designed for medium-to-high divergent eukaryotic genomes (not bacteria)
SyMAP System Guide - University of Arizona SyMAP can also align genomes represented by an FPC physical map, by first aligning the BACs using BAC-end sequences or marker sequences If you plan to work with FPC alignments, the first step is to run the provided demo "Demo-FPC"
SyMAP User Guide - University of Arizona Using the hits that pass the Stage 1 filters, SyMAP constructs putative gene families (PgeneFs) spanning the selected species This is done by grouping hits whose hit regions overlap on at least one genome
SyMAP v5 Download - agcol. arizona. edu Please complete the following registration form to download the SyMAP package The information is only used to track usage The download includes sample data and is 136Mb in size
SyMAP Tour - agcol. arizona. edu SyMAP includes powerful search features to help make the most of synteny information Aligned regions across the selected species are automatically grouped into "putative gene families" The filters allow you to locate the families of interest based on annotation, level of synteny, and presence or absence in different lineages
SyMAP Docs - agcol. arizona. edu This site will stay active indefinitely since the SyMAP pre-v5 1 0 releases reference these pages This download and documentation is for a SyMAP version that includes FPC maps
MUMmer with SyMAP - University of Arizona SyMAP will select the correct directory for the machine you are running from, i e you do not need to do anything When SyMAP creates a database, it (1) checks the MySQL variables, and (2) checks that the external programs are executable
SyMAP Trouble - University of Arizona A message at startup means SyMAP was not able to connect to the database using the provided information in symap config First, make sure your db_adminuser and db_adminpasswd are correct These days, the best way to find the MySQL problems is to search the internet
AGCoL SyMAP Synteny mapping and analysis program Compute the synteny between two sequences genomes or a sequenced genome and FPC map Query and view two or more genomes at a time
SyMAP Demo - University of Arizona SyMAP Demo-Seq to Demo-Seq2 This document shows the different views for the Demo-Seq to Demo-Seq2 alignment When synteny has been computed for the demo, the table will have a checkbox, signifying that the synteny is available for viewing