Multiple alignment part is shown as follows.
If you click link (7), flat file of accession number you selected is shown.
The function is the same as (5).
The entry comment in the retrieval result of the PDB data base is displayed by the
following compositions.
>1TLA |2.0 | 1| 164|M|LYSOZYME (E.C.3.2.1.17) (MUTANT WITH CYS...
______ ____ __ ____ _ ____________________________________________
(a) (b) (c) (d) (e) (f)
(a) : PDB ID CODE ( + Chain Identify)
(b) : RESOLUTION (Numeric value:X-RAY, "NOT":NMR)
(c) : NUMBER OF CHAINS (1:Monomer, 2:Dimer, 3:Trimer...)
(d) : NUMBER OF RESIDUES
(e) : MUTANT (M:Mutant, N:Probably Native)
(f) : PROTEIN NAME
Graphical View
How to see "Graphical View" is shown as follows.
(8) Up to 100 alignments can be seen graphically when "Graphical View" is checked.
The top bar in blue represents the query sequence whose length is shown by a scale.
Colored arrows indicate regions and directions of sequences matched to the query sequence.
By clicking these arrows, you can jump to multiple alignment part.
Furthermore, you can easily transfer sequences to CLUSTALW analysis by checking the boxes
on the left side of each arrow, and then click "CLUSTALW SETUP".
Please use "Text View" when you want to select 100 or more.
The following message is displayed when sequences are 100 or more. (XXX is the entire number. )
** WARNING: ONLY 100 SEQUENCES OUT OF XXX ARE SHOWN. TO SELECT MORE THAN 100 SEQUENCES, GO TO Text View.
Please use "Text View" when you want to select 100 or more.
If you use check box (9), you can select sequences that wants to be analyzed with CLUSTALW.
It is possible to select it by the addition after clicking SELECT button. But when the SELECT button is pushed after (9), the check on (9) becomes invalid.
When blastx or tblastx is selected, Query cannot be selected.
If you specifies the condition by using (10), sequences can be selected.
-
| * |
(a) |
You select one either of Value or Score, specify the value, and click the SELECT button. Then, satisfied sequences are selected. |
| |
(b) |
About Overlapping Positions, you specify the position of Query, and select "Entirely" or "Partially", and click SELECT button.
Then, satisfied sequences are selected.
(You select "Entirely", and if input ranges are included entirely, the sequences are selected.
In one side, you select "Partially" and if input ranges are included partially, the sequences are selected.
If you input only one text box, sequences including the input position is selected.)
|
| |
(c) |
In addition, it is also possible to specify "AND" or "OR" for a compound condition between the condition of E Value or Score and
the condition of Overlapping Positions.
When only either condition is used, both of the specification of "AND" and "OR" are the same treatments.
|
| * |
If you click SELECT button (d), the specified condition is given priority, and selected again.
The function doesn't operate if you do not specify any condition.
When the SELECT button is pushed after (9), the check on (9) becomes invalid.
However, it is possible to add by (9) after the SELECT button is pushed. |
If you click button (11), CLUSTALW SETUP is shown.
The FASTA format sequences you selected is set in text box of CLUSTALW.
Multiple Alignment
How to see "Multiple Alignment" is shown as follows.
This opens from "Show Multiple Alignment" of link in the upper part of the BLAST retrieval result.
When GAP is off and blastn or blastp or tblastn is selected, this is shown.
(12) A whole of multiple alignment is shown.
The part of "-" shows that the sequence becomes a hit.
The part of "=" shows that two or more sequences become a hit.
(13) A detail of multiple alignment is shown.
It is shown that the part of "." is corresponding to Query of BLAST.
CLUSTALW SETUP
How to see "CLUSTALW SETUP" is shown as follows.
This opens from "CLUSTALW SETUP" of link in the upper part of the BLAST retrieval result.
CLUSTALW SETUP(Graphical View) is selected
(14) Up to 100 alignments can be seen graphically when "Graphical View" is checked.
The top bar in blue represents the query sequence whose length is shown by a scale.
Colored arrows indicate regions and directions of sequences matched to the query sequence.
By clicking these arrows, you can jump to the respective alignments.
Furthermore, you can easily transfer sequences to CLUSTALW analysis by checking the boxes
on the left side of each arrow, and then click "CLUSTALW SETUP".
Please use "Text View" when you want to select 100 or more.
The following message is displayed when sequences are 100 or more. (XXX is the entire number. )
** WARNING: ONLY 100 SEQUENCES OUT OF XXX ARE SHOWN. TO SELECT MORE THAN 100 SEQUENCES, GO TO Text View.
Please use "Text View" when you want to select 100 or more.
If you use check box (15), you can select sequences that wants to be analyzed with CLUSTALW.
It is possible to select it by the addition after clicking SELECT button. But when the SELECT button is pushed after (15), the check on (15) becomes invalid.
When blastx or tblastx is selected, Query cannot be selected.
If you specifies the condition by using (16), sequences can be selected.
-
| * |
(a) |
You select one either of Value or Score, specify the value, and click the SELECT button. Then, satisfied sequences are selected. |
| |
(b) |
About Overlapping Positions, you specify the position of Query, and select "Entirely" or "Partially", and click SELECT button.
Then, satisfied sequences are selected.
(You select "Entirely", and if input ranges are included entirely, the sequences are selected.
In one side, you select "Partially" and if input ranges are included partially, the sequences are selected.
If you input only one text box, sequences including the input position is selected.)
|
| |
(c) |
In addition, it is also possible to specify "AND" or "OR" for a compound condition between the condition of E Value or Score and
the condition of Overlapping Positions.
When only either condition is used, both of the specification of "AND" and "OR" are the same treatments.
|
| * |
If you click SELECT button (d), the specified condition is given priority, and selected again.
The function doesn't operate if you do not specify any condition.
When the SELECT button is pushed after (15), the check on (15) becomes invalid.
However, it is possible to add by (15) after the SELECT button is pushed. |
If you click button (17), CLUSTALW SETUP is shown.
The FASTA format sequences you selected is set in text box of CLUSTALW.
CLUSTALW SETUP(Text View) is selected
(18) Alignments can be seen by arrows of the text.
The arrow indicates the range and direction of sequence that becomes a hit.
The uppermost part shows QUERY, and a right and left scale shows the range of QUERY.
If you use check box (19), you can select sequences that wants to be analyzed with CLUSTALW.
It is possible to select it by the addition after clicking SELECT button. But when the SELECT button is pushed after (19), the check on (19) becomes invalid.
When blastx or tblastx is selected, Query cannot be selected.
If you specifies the condition by using (20), sequences can be selected.
-
| * |
(a) |
You select one either of Value or Score, specify the value, and click the SELECT button. Then, satisfied sequences are selected. |
| |
(b) |
About Overlapping Positions, you specify the position of Query, and select "Entirely" or "Partially", and click SELECT button.
Then, satisfied sequences are selected.
(You select "Entirely", and if input ranges are included entirely, the sequences are selected.
In one side, you select "Partially" and if input ranges are included partially, the sequences are selected.
If you input only one text box, sequences including the input position is selected.)
|
| |
(c) |
In addition, it is also possible to specify "AND" or "OR" for a compound condition between the condition of E Value or Score and
the condition of Overlapping Positions.
When only either condition is used, both of the specification of "AND" and "OR" are the same treatments.
|
| * |
If you click SELECT button (d), the specified condition is given priority, and selected again.
The function doesn't operate if you do not specify any condition.
When the SELECT button is pushed after (19), the check on (19) becomes invalid.
However, it is possible to add by (19) after the SELECT button is pushed. |
If you click button (21), CLUSTALW SETUP is shown.
The FASTA format sequences you selected is set in text box of CLUSTALW.
CLUSTALW SETUP
(22) The FASTA format sequences you selected is set.
Last updated: Sep. 05, 2011
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