Help
Quick Search
Quick search allows keywords searches to performed on all text fields:
- Identify the keywords of interest for your search.
- Enter the terms (or key concepts) in the search box.
- Click "Quick Search".
Text Search
The Simple Search page allows you to search individual fields found within signal peptide.
- Find the index field in the menu and combine them.
- Enter the appropriate contents in the text area below.
- Click "Submit" (or click "Reset" to clear your input).
BLAST
The BLAST (Basic Local Alignment Search Tool) program uses a strategy based on matching sequence fragments by employing a powerful statistical model to find the best local alignments (For more information see http://www.ebi.ac.uk/Tools/sss/ncbiblast/).
Usage Introduction
Step 1 – Sequence Input
- Sequence Input Window: The query sequence can be entered directly into text area. The sequence must be FASTA format.
FASTA format: FASTA formatted sequence records start with a definition line, which must start with a > character. The definition line must occupy one single line and followed by sequence data.
Example:
>
FLPLLAGLAANFLPTIICKISYKC
Step 2 – Parameters
- Matrix: This option allows you to choose the scoring matrix to be applied to the search.
Default value is: BLOSUM62
Tip: In general, higher value BLOSUM matrices (e.g. BLOSUM90) and lower value PAM matrices (e.g. PAM30) are more stringent than low value BLOSUM or high value PAM matrices. This implies that if you want to find more distantly related homologues, you should preferentially employ a low value BLOSUM or high value PAM matrix (For more information about scoring matrices see http://en.wikipedia.org/wiki/Matrix).
Foldseek
Foldseek allows SPKB to be searched using sequences or structures. Output display options include BLAST-TAB or Pretty HTML (available only when the input is structure).
Usage Introduction
Step 1 – Sequence Input or PDB/CIF File load
- Sequence Input Window: The query sequence can be entered directly into text area. The sequence must be FASTA format.
FASTA format: FASTA formatted sequence records start with a definition line, which must start with a > character. The definition line must occupy one single line and followed by sequence data.
Example:
>
FLPLLAGLAANFLPTIICKISYKC
Step 2 – Output format:
- Output format: This option allows you to choose the Output format to be applied to the search.
Default value is: BLAST-TAB
