医学信息分析-Chapter-2-Genome-alignment-and-assembly-

1、Chapter 2 genome alignment and assemblyQ1如果要把所测的DNA序列与参考基因组进行比较，请你尽可能的列举出所有的难点。SOAP rulesSOAP will allow either a certain number of mismatches or one continuous gap for aligning a read onto the reference sequence.The best hit of each read which has minimal number of mismatches or smaller gap will be

2、 reported. For multiple equal best hits, the user can instruct the program to report all, or randomly report one, or disregard all of them.SOAP rulesthe program will allow at most two mismatches.occurrence of single nucleotide polymorphism is much higher than that of small insertions or deletions, s

3、o ungapped hits have precedence over gapped hits.For gapped alignment only one continuous gap with a size ranging from 1 to 3 bp is accepted, while no mismatches are permitted in the flanking regions to avoid ambiguous gaps. SOAP rulesSOAP can iteratively trim several basepairs at the 3-end and redo

4、 the alignment, until hits are detected or the remaining sequence is too short for specific alignment.SOAP (Pair-end sequencing)Pair-end sequencing means to sequence both ends of a DNA fragment. So the two reads belonging to a pair will always have the settled relative orientation and approximate di

5、stance between each other on the genome.A pair will be aligned when two reads are mapped with the right orientation relationship and proper distance.A certain number of mismatches are allowed in one or both reads of the pair. For gapped alignment, gap is only permitted on one read, and the other end

6、 should match exactly.SOAPoptionsInputquery a file, *.fq or *.fa formatreference sequences file, *.fa formatoutput alignment fileseed size, default=10. read18,s=8; read22,s=10, read26, s=12maximum number of mismatches allowed on a read, =5. default=2bpmaximum gap size allowed on a read, default=0bpS

7、OAPoptionsInputmaximum number of equal best hits to count, smaller will be faster, n Ns, default=5how to report repeat hits, 0=none; 1=random one; 2=all, default=1do alignment on which reference chain? 0:both; 1:forward only; 2:reverse only. default=0number of processors to use, default=1SOAP(Option

8、s for pair-end alignment:)Inputquery b fileminimal insert size allowed, default=400maximal insert size allowed, default=600output file of unpaired alignment hitsSOAP(Options for miRNA alignment:)Input3-end adapter sequence, default=not miRNA number of mismatch allowed in adapter, default=0 minimum l

9、ength of a miRNA, default=17 maximum length of a miRNA, default=26 SOAP(Format of output)Outputid of read; full sequence of read. the read will be converted to the complementary sequence if mapped on the reverse chain of reference; number of equal best hits.length of the read, if aligned after trimm

10、ing, it will report the information of trimmed read; alignment on the direct(+) or reverse(-) chain of the reference;SOAP(Format of output)Outputid of reference sequence;location of first bp on the reference, counted from 1; type of hits.0: exact match.1100 RefAllele-OffsetQueryAlleleQual: number of

11、 mismatches, followed by detailed mutation sites and switch of allele types. Offset is relative to the initial location on reference.OffsetAlleleQual: offset, allele, and quality.FeaturesThere are limitations to the alignment approach, such as placing reads within repetitive regions in the reference

12、 genome or in corresponding regions that may not exist in the reference genome; the latter situation may result from gaps in the reference genome or the presence of structural variants (SVs) in the genome being analysed.mate-pair reads can resolve the correct genome assignment for some repetitive re

13、gions as long as one read in the pair is unique to the genomeIndexFor the readsFor the ReferenceFor bothBased on hash tablesBased on suffix treesBased on merge sortingAlgorithms based on hash tablesATCCGAATCCCATGGGAAAGCTATACGTTAGGCCATGCCATGACHash TableK-mer (11) PositionATCCGAATCCCGGCAHDe novo assembliessubstantial challenges exist for their application to