SeWeR: Database Searches
Author: Malay

Select the program of choice. Paste your query in the query box. Click Submit button to pass on the query with default options. Please note that some programs might have some options/parameters that are required. Also note that SeWeR doesn't check whether the required option(s)/parameter(s) is supplied or not. See program description for details. Click Options button to fill up options. The button is a toggle. Clicking it again will close the option. Click Customize to customize this search. Fill up all the options that you require, then click Customize. SeWeR will open another window with a customized page. Save that file on your computer. Click Help to check the help page of the selected program. SeWeR will open a new window to show the help page. Click Submit to pass on the query. SeWeR will open a new window for results.
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pubmed
Field | only items with abstracts
Publication Type | Language
Entrez date | Subsets
Date From To Use the format YYYY/MM/DD; month and day are optional.

blocks search |
Email (optional) | Database |
Cutoff expected value | Amount of output |
Sequence type |
For DNA Query |
Strands to search | Genetic code |

scanprosite
SWISS-PROT/TrEMBL accession number or a sequence identifier
Exclude patterns with a high probability of occurrence

PubMed |
Search bibliographic database at NCBI. Input type-key-word. Can accept boolean search. Required option-none.

Blocks Searcher |
Search BLOCKS database for similarity. Input type- protein or DNA sequence. Required options-none.

ScanProsite |
Search for PROSITE pattern in your protein sequence. Input type-protein sequence. Required option-none.

BLASTP |
Search a protein sequence against the protein sequences on NCBI server. Query type-Protein Sequence. Required option- none

blastp Set subsequence: From To Database Do CD-search Limit by Entrez query or select from Composition based statistics Choose Filter: Low complexity Mask for lookup table only Mask lower case Expect Word Size Matrix Gap cost PSSM Other Advanced option PHI pattern Show overview NCBI GI Show Format Number of descriptions Number of alignments Alignment view Format for PSI-BLAST with inclusion threshhold Layout Format on the result page Autoformat Send result by e. mail

BLASTN |
Search a nucleotide sequence against GenBank on NCBI server. Query type: DNA sequence. Required option: None.

blastn Set subsequence: From To Database Limit by Entrez query or select from Choose filter: Low complexity Human repeats Mask for lookup table only Mask lower case Expect Word size Other advanced option Show: graphical overview NCBI-GI Format type Number of descriptions Number of alignments Alignment view Layout Formatting options on page with results Autoformat Send results by e-mail

Translated BLAST |
Translated BLAST are a set of BLAST programs that first translate your DNA sequence and searches database of protein sequence/ translated nucleotide sequence. Default program BLASTX.Query type: DNA sequence. Required option: none.

Translated BLAST Choose program Set subsequence: From To Choose database Genetic code Limit by Entrez query or select from Choose filter Low complexity Mask for lookup table only Mask lower case Expect Word Size Matrix Gap cost Other advanced option Show: overview NCBI-GI Format Number of descriptions Number of alignments Alignment view Layout Formatting options on page with results Autoformat Send results by e-mail