SyMAP v3.4: a turnkey synteny system with application to plant genomes

By Carol Soderlund, Matthew Bomhoff, William M. Nelson. Nucleic Acids Research, 2011

308 citations recorded by the source corpus.

SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes. SyMAP uses MUMmer to compute the raw hits between the two genomes, which are then clustered and filtered using the optional gene annotation. The filtered hits are input to the synteny algorithm, which was designed to discover duplicated regions and form larger-scale synteny blocks, where intervening micro-rearrangements are allowed. SyMAP provides extensive interactive Java displays at all levels of resolution along with simultaneous displays of multiple aligned pairs. The synteny blocks from multiple chromosomes may be displayed in a high-level dot plot or three-dimensional view, and the user may then drill down to see the details of a region, including the alignments of the hits to the gene annotation. These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice. The software may be used from a website or standalone for the best performance. A project manager is provided to organize and automate the analysis of multi-genome groups. The software is freely distributed at http://www.agcol.arizona.edu/software/symap.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/b897292f10b7e78c21e694267376484d37515549

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Plant Science

Citations in the corpus

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. (2011, background): “Pairs of sequences with high similarity (identity >60% and aligned coverage >500 bp) were selected to check for synteny between Medicago and soybeans by comparing their locations to syntenic blocks between Medicago and soybeans detected by SyMAP (Soderlund et al. 2011).”
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity (2012, background): “…(15), OrthoCluster (16), DiagHunter (69), DAGChainer (17), ColinearScan (18), MCScan (19), SyMAP (20), FISH (21), Cyntenator (22), MicroSyn (28) and Cinteny (70), of which OrthoCluster, ADHoRe and SyMAP are currently upgraded to OrthoClusterDB (71), i-ADHoRe 3 (72) and SyMAP 3.4 (73), respectively.”
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, methodology): “In addition to the approaches discussed above, several methods have also been developed that incorporate gene synteny/co-linearity information to assist in the inference of orthogroups [16, 17].”