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

2. AMOS file format (.afg) {FRG iid:456 eid:90 lib:453 rds:88,89 typ:I }
This “fragment” is a clone insert, from which
both ends have been sequenced
{FRG
iid:456
eid:90
lib:453
rds:88,89
typ:I }
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

3. AMOS file format (.afg) This is read ID 88
{RED
iid:88
eid: f
seq:
GCCACGTAGGCGTTTTGGATGGAAATTAGCCGCCTCGGGCGTCGCATTGCTCAAGGGACTAATTTCAGCG
GCCCTGTGATGTGGCCTGTCGGTGGGGGTGTGGTGAGGAGTTCGCGAACCTGATCGTCGAGTAGATCTGT
CCAACCGTCATCAAACGCGGATATCAATGGGTTGCGCACACCACATCGTAGGCTTCGTGCGATCTCACGG
CCAGGCTGGCTGTTGGCCCGACCGGTATCGTGACAATTATTGATTTGGGGGGTCGAGCGGGTCTCGTGGC
CCGTAAGTTACGGTACGGCGGCCGTCAGCATGCTGGCGCCGGTGGCTATGCCGTCATCGACGGGGGTCAC
GGTCCTGCCGTGTGGGTCGGCCGACGGTGCGCTTGCCCCTATACATCCGTTTGCATCGCATGAGTGCCAC
TGTCTCCTTGTCAATCACTCGTGCGAGTCAGCATCGGACGGGGCATTGTTGGGGTATTGAGGCCTTGGGT
GGTGGTGTTGTG .
qlt:
KKKKK7IK:KKKKKKA9KKKKKKKK5KKKKKKKT;KKKKQKLKKKKKKFKKKK<E<K:KKKKNKK9KK9=
KKKKKKKTKKK5FKKKKKKKKKKUKKKKKKKK8RKKKQTKKKFKKPSKKKKKK:KKKKKKKK<KKOKKK=
KPKKKKKKKKKIHBKKKK<NKBKKKKK;KKKKK6DKKKKK=KKKKSKKKKKUKKEKKKKKKHKPIKRKKG
KKKKKKK9KKKKKKK;KK7KTNKQKKKKKKKKJBKNKUKK7K99OKKKKK7KKKKKKDKKKKKPK7HAKK
KKKKKKUTKUKK
frg:456
clr: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

4. Lab2: identifying the species
just BLAST it
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 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