AMOS file format 'afg

1
AMOS file format (.afg)
LIB iid453 eid17000001585820 DST mea3000.000
std166.667
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
AMOS file format (.afg)
FRG iid456 eid90 lib453 rds88,89 typI
3
AMOS file format (.afg)
RED iid88 eid17000001585880f
seq GCCACGTAGGCGTTTTGGATGGAAATTAGCCGCCTCGGGCGTCG
CATTGCTCAAGGGACTAATTTCAGCG GCCCTGTGATGTGGCCTGTCGGT
GGGGGTGTGGTGAGGAGTTCGCGAACCTGATCGTCGAGTAGATCTGT CC
AACCGTCATCAAACGCGGATATCAATGGGTTGCGCACACCACATCGTAGG
CTTCGTGCGATCTCACGG CCAGGCTGGCTGTTGGCCCGACCGGTATCGT
GACAATTATTGATTTGGGGGGTCGAGCGGGTCTCGTGGC CCGTAAGTTA
CGGTACGGCGGCCGTCAGCATGCTGGCGCCGGTGGCTATGCCGTCATCGA
CGGGGGTCAC GGTCCTGCCGTGTGGGTCGGCCGACGGTGCGCTTGCCCC
TATACATCCGTTTGCATCGCATGAGTGCCAC TGTCTCCTTGTCAATCAC
TCGTGCGAGTCAGCATCGGACGGGGCATTGTTGGGGTATTGAGGCCTTGG
GT GGTGGTGTTGTG . qlt KKKKK7IKKKKKKKA9KKKKKKKK5K
KKKKKKTKKKKQKLKKKKKKFKKKKltEltKKKKKNKK9KK9 FKltKKK
_at_KKLKOKKKKKKKKKJK5?KKKKMLKKK8IKKTKKKKF_at_KKTKKK5_at_U
KBKKUADDKKEKHlt EKDUKKKKPKKKBKK9TKKPKK_at_?KKGKKKKKKK
KTKKKKKUK9KKKgtLK5KKKKK9KK8KFOKKKQK KKKKKKKTKKK5FK
KKKKKKKKKUKKKKKKKK8RKKKQTKKKFKKPSKKKKKKKKKKKKKKltK
KOKKK KPKKKKKKKKKIHBKKKKltNKBKKKKKKKKKK6DKKKKKKK
KKSKKKKKUKKEKKKKKKHKPIKRKKG KOKKMKKKKKKKK5KgtKKOKS6
KKCKKSKltKKKN_at_TKKKKK?QKKKgtPKgtKLGKKKKKKKKMUKKDKKK K
KKKKKK9KKKKKKKKK7KTNKQKKKKKKKKJBKNKUKK7K99OKKKKK7
KKKKKKDKKKKKPK7HAKK KKKKKKUTKUKK . frg456 clr0,5
02
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