AMOS file format (.afg)
{LIBiid:453eid:17000001585820{DSTmea:3000.000std: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
AMOS file format (.afg)
{FRGiid:456eid:90lib:453rds:88,89typ:I}
Its internal ID is 456
This “fragment” is a clone insert, from whichboth ends have been sequenced
It came from Library 453 (which hasan insert length of 3000bp)
Its ends are identified by the two readswith internal IDs 88 and 89
Its ends face “Inward”, 5’ on the outsideand 3’ on the inside
AMOS file format (.afg)
{REDiid:88eid:17000001585880f seq:GCCACGTAGGCGTTTTGGATGGAAATTAGCCGCCTCGGGCGTCGCATTGCTCAAGGGACTAATTTCAGCGGCCCTGTGATGTGGCCTGTCGGTGGGGGTGTGGTGAGGAGTTCGCGAACCTGATCGTCGAGTAGATCTGTCCAACCGTCATCAAACGCGGATATCAATGGGTTGCGCACACCACATCGTAGGCTTCGTGCGATCTCACGGCCAGGCTGGCTGTTGGCCCGACCGGTATCGTGACAATTATTGATTTGGGGGGTCGAGCGGGTCTCGTGGCCCGTAAGTTACGGTACGGCGGCCGTCAGCATGCTGGCGCCGGTGGCTATGCCGTCATCGACGGGGGTCACGGTCCTGCCGTGTGGGTCGGCCGACGGTGCGCTTGCCCCTATACATCCGTTTGCATCGCATGAGTGCCACTGTCTCCTTGTCAATCACTCGTGCGAGTCAGCATCGGACGGGGCATTGTTGGGGTATTGAGGCCTTGGGTGGTGGTGTTGTG.qlt:KKKKK7IK:KKKKKKA9KKKKKKKK5KKKKKKKT;KKKKQKLKKKKKKFKKKK<E<K:KKKKNKK9KK9=FK<KKK@KKLKOKKKKK:KKKKJK5?KKKKMLKKK8IKKTKKKKF@KKTK=KK5@UKBKKUADDKKEKH<EKDUKKK;KPKKKBKK9TKKPKK@?KKGKKKKKKKKTKKKKKUK9KKK>LK5KKKKK9KK8KFO;KKKQKKKKKKKKTKKK5FKKKKKKKKKKUKKKKKKKK8RKKKQTKKKFKKPSKKKKKK:KKKKKKKK<KKOKKK=KPKKKKKKKKKIHBKKKK<NKBKKKKK;KKKKK6DKKKKK=KKKKSKKKKKUKKEKKKKKKHKPIKRKKGKOKKMKKKKKKKK5K>KKOKS6:KKCKKSK<KKKN@TKKKKK?QKKK>PK>KLGKKKKKKKKMUKKDKKKKKKKKKK9KKKKKKK;KK7KTNKQKKKKKKKKJBKNKUKK7K99OKKKKK7KKKKKKDKKKKKPK7HAKKKKKKKKUTKUKK.frg:456clr:0,502}
This is read ID 88
It comes from fragment (pair) 456
The high-quality (“clear”) part of the read is from 0-502
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.
Running AMOScmp
Input files: lab02.afg, lab02.1con
$ AMOScmp lab02The log file is: lab02.runAmos.logDoing step 10: Building AMOS bankDoing step 20: Collecting clear range sequencesDoing step 30: Running nucmerDoing step 40: Running layoutDoing step 50: Running consensusDoing step 60: Outputting contigsDoing step 70: Outputting fasta
Files created:lab02.bnk (a directory)lab02.conflictlab02.delta (created by nucmer)lab02.layoutlab02.seqlab02.cluster (created by nucmer)lab02.contiglab02.fastalab02.runAmos.log
Human duplicationsArabidopsis thaliana duplications
