Assigning Contig to Chromosome

Assign Contig to Chromosome for FPC V7

This also applies to Linkage groups. Just replace the word chromosome with linkage group.

The following are considered 'evidence':

SD (simulated digest of sequenced clones) may contain a chromosome number as extracted from Genbank.
Each anchor is associated with a chromosome. The anchors are any set of ordered markers. They are generally from a genetic map or radiation hybrid map. There is two types: Frameworks (FW) are well ordered, and Placements (PM) are binned between the frameworks and the order is not so precise. Note: the term framework is often used in place of the work anchor to indicate the whole set.

FPC V7 allows the user to define what rules will be used for assigning contigs to chromosomes. The AGI/AGCoL projects use the defaults, as follows:

When evaluating each contig, each SD clone and FW marker counts as two points for a chromosome, and a PM marker counts as one point. The chromosome with the most points is the 'winning' chromosome and the contig is assigned to that chromosome. For example, a contig remark:

        Chr1 [4 chr8/1 chr6/1 Fw3 Pm3]

says the chr1 has 4 pieces of evidence. Chr8 and chr6 both have one piece. There is a total of 6 pieces of evidence, 3 are frameworks and 3 are placements.

If only a single anchors (frameworks or placements) hits a contig, it is ignored if they only hit one clone, or anchor multiple contigs. If the anchor that hits one clone is the only piece of evidence, the remark will have the format:

        -  [ Chr4-1 Fw1]

indicating that there is one framework on Chr4 with one clone. The '-' indicates this situation. If the anchor hits multiple chromosome and is the only piece of evidence, the remark will have the format:

        &  [ chr7/AY000]

where AY000 is the name of the offending marker.

Also, for each chromosome, the number of clone hits is counted. That is, the sum of clone hits for all frameworks for a given chromosome plus the SD clones. Contigs are not assigned to any chromosome if the number of clone hits to the winning chromosome is less than half the number of hits to the clones hitting other chromosomes. In other words, if

 hits to clones for winning contig < (sum of all other hits to clones * 2)

For example,

        +  [ Chr/1 Chr6/1 Fw2]

is the chromosome remark. It is not assigned a chromosome because:

  Chr1  total  1  Fw  1  Seq   0  clones  6 
  Chr6  total  1  Fw  1  Seq   0  clones  5

The '+' indicates this situation ambiguous situation.

Maximum between anchors: First, the algorithm wil calculate what chromosome a contig belongs on by the above rules. It then evaluated the anchors for that chromosome; if all of them are greater than the specified distance, the contig is not assigned. For example,

 
       !   [ ch1-2 ch2-3 Fw3]

It would have been assigned to Chr1, except the two anchors were too far apart.

When the FPC file is being edited manually, the editor may want to override the FPC ctg->chr assignment. The contig is marked as such, and the editor puts in the chromosome assignment. In this case, the assignment function will put the FPC generated assignment in brackets. For example,

  Chr2 {...2 [4 ch3/1 Fw3 Pm2]}
  Chr4 {+    [ ch4/2 ch9/2 ch2/1 ch10/1 Fw4 Pm2]}

The chromosome assignment is provided by the editor, in brackets is the FPC assignment.

These contig remarks are not shown in WebFPC, though the chr/lg assignment is.