1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
|
<HTML>
<TITLE>Blocks Searcher Email Server Options</TITLE>
<H1>Blocks Searcher Email Server Options</H1>
<B>Please note:</B> The Blocks Searcher Email Server will soon be
discontinued. For searching a few queries, supply your email address
on the
<A HREF="/blocks/blocks_search.html">Block Searcher form</A>.
Here is a
<A HREF="bulk_search.txt">sample perl script</A>
to do bulk searches.<P>
<HR>
Blocks Email Searcher:
<A HREF="mailto:blocks@blocks.fhcrc.org">blocks@blocks.fhcrc.org</A>
<BR><A HREF=#EXAMPLES>Examples</A> of the new options follow.
<P>
<B>Please note:</B> Please send clear text only.
<P>
<B>Please note:</B> Effective 2 May 2002 the #SQ option is required.
<P>
<B>Please note:</B> <A HREF=#DEFAULT>Default options</A> will be used
if the message consists solely of a sequence.
<P>
<B>Please note:</B> If you want to put comments in the message,
start them with # in the first column and put them before the
sequence, being careful not to start your comment with any of
the reserved words listed below. Nothing should follow the sequence.
<P>
Searching options:
<UL>
<P><LI>
Database to search:<BR>
<PRE>
#DB PLUS(default) | MINUS(PLUS without biased blocks) | PRINTS
</PRE>
<P><LI>
Query sequence type:<BR>
<PRE>
#TY AUTO(default) | AA | DNA
</PRE>
<P><LI>
For DNA queries, strands to search:<BR>
<PRE>
#ST BOTH(default) | FORWARD | REVERSE or 2 | 1 | -1
</PRE>
<P><LI>
For DNA queries, genetic code to use for translation:<BR>
<PRE>
#GE 0(default) to 8
</PRE>
</UL>
Post-processing options:
<UL>
<P><LI>
Output type:<BR>
<PRE>
#OU ALL(default) | SUM | GFF | OLD | RAW
</PRE>
<P><LI>
Output format:<BR>
<PRE>
#FO TEXT(default) | HTML
</PRE>
<P><LI>
Expected value cutoff:<BR>
<PRE>
#EX n (default=5)
</PRE>
</UL>
Sequence definition (required):
<UL>
<PRE>
#SQ
Sequence in fasta or other common formats.
<B>WARNING:</B> Everything after #SQ is treated as sequence, so do not
append any signature, etc.
</PRE>
</UL>
<HR>
<A NAME="EXAMPLES">Examples</A>:
<PRE>
1. <A NAME="DEFAULT">Old defaults</A>; result of just mailing sequence
with no lines beginning with "#":
#DB plus
#TY auto
#ST 2
#GE 0
#OU old
#FO text
#SQ
>SPRE_RAT SEPIAPTERIN REDUCTASE (EC 1.1.1.153) (SPR)
MEGGRLGCAV CVLTGASRGF GRALAPQLAG LLSPGSVLLL SARSDSMLRQ LKEELCTQQP
GLQVVLAAAD LGTESGVQQL LSAVRELPRP ERLQRLLLIN NAGTLGDVSK GFLNINDLAE
VNNYWALNLT SMLCLTTGTL NAFSNSPGLS KTVVNISSLC ALQPFKGWGL YCAGKAARDM
LYQVLAVEEP SVRVLSYAPG PLDTNMQQLA RETSMDPELR SRLQKLNSEG ELVDCGTSAQ
KLLSLLQRDT FQSGAHVDFY DI
2. New searching/post-processing defaults
#DB plus
#TY auto
#ST 2
#GE 0
#EX 5
#OU all
#FO text
#SQ
>SPRE_RAT SEPIAPTERIN REDUCTASE (EC 1.1.1.153) (SPR)
MEGGRLGCAV CVLTGASRGF GRALAPQLAG LLSPGSVLLL SARSDSMLRQ LKEELCTQQP
GLQVVLAAAD LGTESGVQQL LSAVRELPRP ERLQRLLLIN NAGTLGDVSK GFLNINDLAE
VNNYWALNLT SMLCLTTGTL NAFSNSPGLS KTVVNISSLC ALQPFKGWGL YCAGKAARDM
LYQVLAVEEP SVRVLSYAPG PLDTNMQQLA RETSMDPELR SRLQKLNSEG ELVDCGTSAQ
KLLSLLQRDT FQSGAHVDFY DI
3. New searching/post-processing options
#DB prints
#TY DNA
#ST 1
#GE 1
#EX 3
#OU sum
#FO html
#SQ
gi|8133541|gb|AW507376.1|AW507376 EST00092 Rattus
ACATCATGGCTCTGACTTGGGTTAAGCTCTTGGCACCAATGTCCTGACAGGAATGCTGGATGCCAGCAAT
CAAATAAGGGACAAACTTGTGGATAGACCCTTTGTCCTGCACTGCCCCTGAAACTCCTTGGGCCACTTTG
ATCTTGTCAGCTTCACTGAAATATCGGTTCTGGCTGCTGAGGTGTTTGTCAAGTACATCAAGGAAAAATA
CCCCAATCTCCAGGTCATCGGAGGCAATGTAGTCACTGCTGCTCAAGCCAAGAACCTCATCGACGCAGGT
GTGGACGCTCTGCGAGTCGGCATGGGAAGTGGTTCCATCTGCATCACCCAGGAAGTGTTGGCCTGTGGGC
GACCCCAAGCAACAGCAGTATACAAGGTCTCTGAGTATGCCCGTCGCTTCGGTGTCCCTGGTATTGCTGA
TGGAGGAAT
</PRE>
</HTML>
|
