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AMOS file format (.afg)

AMOS file format (.afg). { LIB iid:453 eid:17000001585820 {DST mea:3000.000 std:166.667 }. This is an insert “library” with mean insert length of 3000bp, and a standard deviation of 166.667 bp. The library ID is 453. This “fragment” is a clone insert, from which

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AMOS file format (.afg)

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  1. AMOS file format (.afg) {LIB iid:453 eid:17000001585820 {DST mea:3000.000 std:166.667 } This is an insert “library” with mean insert length of 3000bp, and a standard deviation of 166.667 bp. The library ID is 453

  2. This “fragment” is a clone insert, from which both ends have been sequenced Its internal ID is 456 It came from Library 453 (which has an insert length of 3000bp) Its ends are identified by the two reads with internal IDs 88 and 89 Its ends face “Inward”, 5’ on the outside and 3’ on the inside AMOS file format (.afg) {FRG iid:456 eid:90 lib:453 rds:88,89 typ:I }

  3. This is read ID 88 It comes from fragment (pair) 456 The high-quality (“clear”) part of the read is from 0-502 AMOS file format (.afg) {RED iid:88 eid:17000001585880f seq: GCCACGTAGGCGTTTTGGATGGAAATTAGCCGCCTCGGGCGTCGCATTGCTCAAGGGACTAATTTCAGCG GCCCTGTGATGTGGCCTGTCGGTGGGGGTGTGGTGAGGAGTTCGCGAACCTGATCGTCGAGTAGATCTGT CCAACCGTCATCAAACGCGGATATCAATGGGTTGCGCACACCACATCGTAGGCTTCGTGCGATCTCACGG CCAGGCTGGCTGTTGGCCCGACCGGTATCGTGACAATTATTGATTTGGGGGGTCGAGCGGGTCTCGTGGC CCGTAAGTTACGGTACGGCGGCCGTCAGCATGCTGGCGCCGGTGGCTATGCCGTCATCGACGGGGGTCAC GGTCCTGCCGTGTGGGTCGGCCGACGGTGCGCTTGCCCCTATACATCCGTTTGCATCGCATGAGTGCCAC TGTCTCCTTGTCAATCACTCGTGCGAGTCAGCATCGGACGGGGCATTGTTGGGGTATTGAGGCCTTGGGT GGTGGTGTTGTG . qlt: KKKKK7IK:KKKKKKA9KKKKKKKK5KKKKKKKT;KKKKQKLKKKKKKFKKKK<E<K:KKKKNKK9KK9= FK<KKK@KKLKOKKKKK:KKKKJK5?KKKKMLKKK8IKKTKKKKF@KKTK=KK5@UKBKKUADDKKEKH< EKDUKKK;KPKKKBKK9TKKPKK@?KKGKKKKKKKKTKKKKKUK9KKK>LK5KKKKK9KK8KFO;KKKQK KKKKKKKTKKK5FKKKKKKKKKKUKKKKKKKK8RKKKQTKKKFKKPSKKKKKK:KKKKKKKK<KKOKKK= KPKKKKKKKKKIHBKKKK<NKBKKKKK;KKKKK6DKKKKK=KKKKSKKKKKUKKEKKKKKKHKPIKRKKG KOKKMKKKKKKKK5K>KKOKS6:KKCKKSK<KKKN@TKKKKK?QKKK>PK>KLGKKKKKKKKMUKKDKKK KKKKKKK9KKKKKKK;KK7KTNKQKKKKKKKKJBKNKUKK7K99OKKKKK7KKKKKKDKKKKKPK7HAKK KKKKKKUTKUKK . frg:456 clr:0,502 }

  4. Lab2: identifying the species just BLAST it http://www.ncbi.nlm.nih.gov/BLAST/ Suggestion: If you want a fast answer, set BLAST to use a word size of 15, and set “expect” to a small value such as 0.00001. Or use Megablast.

  5. Running AMOScmp Input files: lab02.afg, lab02.1con $ AMOScmp lab02 The log file is: lab02.runAmos.log Doing step 10: Building AMOS bank Doing step 20: Collecting clear range sequences Doing step 30: Running nucmer Doing step 40: Running layout Doing step 50: Running consensus Doing step 60: Outputting contigs Doing step 70: Outputting fasta Files created: lab02.bnk (a directory) lab02.conflict lab02.delta (created by nucmer) lab02.layout lab02.seq lab02.cluster (created by nucmer) lab02.contig lab02.fasta lab02.runAmos.log

  6. Arabidopsis thaliana duplications Human duplications

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