ÿþBG5B
31.10.09

1.  01>B0 A ?@>3@0<<>9 getorf ?0:5B0 EMBOSS
><0=4=0O AB@>:0 4;O ?>;CG5=8O =01>@0 B@0=A;OF89 2A5E >B:@KBKE @0<>: 40==>9 ?>A;54>20B5;L=>AB8 (70?8A8 D89965 87 
10=:0 EMBL) 4;8=>9 1>;55 30 =C:;5>B84>2, >B:@KB>9 @0<:>9 AG8B0;0AL ?>A;54>20B5;L=>ABL B@8?;5B>2, =0G8=0NI0OAO A> 
AB0@B-:>4>=0 8 70:0=G820NI0OAO AB>?-:>4>=><; 8A?>;L7>20;AO 10:B5@80;L=>3> :>40:

getorf embl:d89965 -minsize 30 -table 11 -find 1 d89965.orf

 D09;5 d89965.orf 5 @0<:0 A>>B25BAB2C5B ?@82545==>9 2 70?8A8 CDS.
0?8A8 SwissProt P0A7B8, =0 :>B>@CN AAK;05BAO 40==0O 70?8AL EMBL, A>>B25BAB2C5B @0<:0 13


3. ><0=4K 70?CA:0:
-megablast 
	megablast -d pm -m 9 -i trna_ecoli.fasta -o megablast_trna_9 -e 0.001
-discontiguous megablast
	megablast -d pm -m 9 -i trna_ecoli.fasta -W 11 -t 16 -N 2 -o megablast_trna_9_1 -e 0.001

4. =0;87 @57C;LB0B>2
3><>;>3, =0945==K9 blastn, => =5 megablast. 3> ?>A;54>20B5;L=>ABL 1K;0 
2K@570=0 2 >B45;L=K9 D09; 4_homologue.fasta. ><>;>3 1K; =0945= 4;O 35=0 valV, 
GLO ?>A;54>20B5;L=>ABL 1K;0 2K@570=0 2 D09; valv.fasta. @8 ?><>I8 ?@>3@0<<K 
needle 1K;> ?@>2545=> 2K@02=820=85 MB8E ?>A;54>20B5;L=>AB59.

%0@0:B5@8AB8:8 2K@02=820=8O:
# 1: valV
# 2: AE006138
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 77
# Identity:      39/77 (50.6%)
# Similarity:    39/77 (50.6%)
# Gaps:          34/77 (44.2%)
# Score: 169.0


valV               1 gcgttcatagctcagttggttagagcaccaccttgacatggtgggggtcg     50
                           ||||||||||||| ||||||||.||||||.||.|||.|||||||
AE006138           1 ------atagctcagttgg-tagagcacaaccttgccaaggttggggtcg     43

valV              51 ttggttcgagtccaattgaacgcacca     77
                                                
AE006138          43 ---------------------------     43


!>3;0A=> >?8A0=8N ?@>3@0<<K megablast, >=0 >?B8<878@>20=0 4;O 2K@02=820=89 
?>A;54>20B5;L=>AB59, A;53:0 >B;8G0NI8EAO 4@C3 >B 4@C30. AE>4O 87 e-value, 
2K40==>3> blastn, @02=><C 15-04, MB8 ?>A;54>20B5;L=>AB8 4>AB0B>G=> A8;L=> 
>B;8G0NBAO, ?>MB><C megablast =5 =0E>48B B0:CN ?0@C.

==>B0F8O 3><>;>30 2 EMBL
FT   gene            1059689..1060003
FT                   /locus_tag="PM0901"
FT   CDS             1059689..1060003
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /locus_tag="PM0901"
FT                   /product="unknown"
FT                   /db_xref="GOA:Q9CMD0"
FT                   /db_xref="UniProtKB/Swiss-Prot:Q9CMD0"
FT                   /protein_id="AAK02985.1"
FT                   /translation="MSIIQAISIFFTFYTCTLAFFSYNVRLSLLNSEKYYAGIAQLVEH
FT                   NLAKVGVASSSLVSRSNISTNQYHILRGNSSVGRAQPCQGWGREFEPRFPLQIFLSNLK
FT                   "