[maker-devel] CIGAR string explanation
Jacques Dainat
jacques.dainat at nbis.se
Tue Oct 23 07:56:09 MDT 2018
Hello,
Here an example of the cigar string output from exonerate (exactly the same command as launched by MAKER)
cigar: P46461.1 3 740 . genome 460484 439594 - 2580 M 84 I 1 D 56 M 154 I 3 M 54 D 1554 M 145 D 3346 M 137 D 120 M 160 D 197 M 182 D 145 M 165 D 415 M 170 D 5037 M 321 D 124 M 158 D 116 M 183 D 1819 M 157 D 5776 M 115
vulgar: P46461.1 3 740 . genome 460484 439594 - 2580 M 28 84 G 1 0 S 0 2 5 0 2 I 0 50 3 0 2 S 1 1 M 51 153 G 3 0 M 18 54 S 0 2 5 0 2 I 0 1548 3 0 2 S 1 1 M 48 144 S 0 1 5 0 2 I 0 3341 3 0 2 S 1 2 M 45 135 S 0 2 5 0 2 I 0 114 3 0 2 S 1 1 M 53 159 S 0 1 5 0 2 I 0 192 3 0 2 S 1 2 M 60 180 5 0 2$
-- completed exonerate analysis
and here the result we get in the protein2genome.gff output from MAKER
@000426F|arrow|arrow protein2genome protein_match 439595 460484 2580 - . ID=@000426F|arrow|arrow:hit:153696:3.10.0.4;Name=P46461.1;target_length=745;aligned_coverage=98.93;aligned_identity=72.6
@000426F|arrow|arrow protein2genome match_part 460399 460484 2580 - . ID=@000426F|arrow|arrow:hsp:233933:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 4 32;Gap=F2 I1 M28
@000426F|arrow|arrow protein2genome match_part 460135 460344 2580 - . ID=@000426F|arrow|arrow:hsp:233934:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 33 105;Gap=F2 M18 I3 M52 R2
@000426F|arrow|arrow protein2genome match_part 458437 458582 2580 - . ID=@000426F|arrow|arrow:hsp:233935:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 106 154;Gap=F1 M49 R2
@000426F|arrow|arrow protein2genome match_part 454953 455091 2580 - . ID=@000426F|arrow|arrow:hsp:233936:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 155 200;Gap=F2 M46 R1
@000426F|arrow|arrow protein2genome match_part 454674 454834 2580 - . ID=@000426F|arrow|arrow:hsp:233937:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 201 254;Gap=F1 M54 R2
@000426F|arrow|arrow protein2genome match_part 454296 454477 2580 - . ID=@000426F|arrow|arrow:hsp:233938:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 255 315;Gap=M61 R1
@000426F|arrow|arrow protein2genome match_part 453985 454150 2580 - . ID=@000426F|arrow|arrow:hsp:233939:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 316 370;Gap=F1 M55
@000426F|arrow|arrow protein2genome match_part 453401 453570 2580 - . ID=@000426F|arrow|arrow:hsp:233940:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 371 427;Gap=M57 R1
@000426F|arrow|arrow protein2genome match_part 448042 448363 2580 - . ID=@000426F|arrow|arrow:hsp:233941:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 428 534;Gap=F1 M107
@000426F|arrow|arrow protein2genome match_part 447761 447918 2580 - . ID=@000426F|arrow|arrow:hsp:233942:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 535 587;Gap=M53 R1
@000426F|arrow|arrow protein2genome match_part 447460 447644 2580 - . ID=@000426F|arrow|arrow:hsp:233943:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 588 648;Gap=F2 M61
@000426F|arrow|arrow protein2genome match_part 445484 445642 2580 - . ID=@000426F|arrow|arrow:hsp:233944:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 649 701;Gap=F2 M53 R2
@000426F|arrow|arrow protein2genome match_part 439595 439709 2580 - . ID=@000426F|arrow|arrow:hsp:233945:3.10.0.4;Parent=@000426F|arrow|arrow:hit:153696:3.10.0.4;Target=P46461.1 702 740;Gap=M39 R2
MAKER apparently process the CIGAR string and save it into the Gap attribute. The value looks like CIGAR string but it is different. Here is the different letters we can find (M, D, I, R, F). I guess M=match, D=deletion and I=insertion, but I don’t get the meaning of the R and F.
Could you explain their meanings ?
Best regards,
/Jacques
-------------------------------------------------
Jacques Dainat, Ph.D.
NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
http://nbis.se/about/staff/jacques-dainat <http://nbis.se/about/staff/jacques-dainat/>
http://nbis.se <http://nbis.se/>
— Contact —
Address: Uppsala University, Biomedicinska Centrum
Department of Medical Biochemistry Microbiology, Genomics
Husargatan 3, box 582
S-75123 Uppsala Sweden
Phone: +46 18 471 46 25
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