Zea mays Mapped Sequence Locator Help
zmMSL is a Web-based BLAST front end for querying map information for a nucleotide sequence.
The current implementation allows for the following parameters from the user:
- query sequence name
- this defaults to 'QuerySequence'
- can be changed to any user meaningfull alphanumeric text string
- NOTE: this name will be used in the display of EACH BLAST hit
- query sequence
- string of characters representing the nucleotide sequence of the query
- cutting and pasting of sequence is the simplest way of entering it into the form
- all non-alphabetic characters entered are stripped from the sequence prior to analysis
- all non-ACGT characters are converted to N's prior to analysis
- database to compare the query sequence to:
- Cornsensus unigene set
- ALL Zea mays sequences from GenBank
- the maximum e-value cut-off for the returned results
- can be set from 10-6 to 1
- higher e-value limits give more results but include lower quality matches
- higher e-value limits can also take marginally longer to process
Note: if no results or only a few results are presented: raising the maximum e-value may yield more results
The blast results are returned in table format:
| GenBank Acc | bit-score | score | e-value |
| QUERYSEQUENCE | <GB ACCESSION> | <BIT-SCORE> | <SCORE> | <E-VALUE> |
| MaizeDB | Linkage Group | Bin | Locus | Coordinate | Backbone | Map |
| < -- results if any here -- > |
| AGI/CUGI | Locus | Probe | AGI Link |
| < -- results if any here -- > |
| ZmDB | Locus | Probe | ZmDB Link |
| < -- results if any here -- > |
| TIGR | Locus | Probe | TIGR Link |
| < -- results if any here -- > |
| Gramene | Locus | Probe | Gramene Link |
| < -- results if any here -- > |
Where the included links provide access to other resources (via information in MaizeDB)
- GenBank - sequence information
- MaizeDB - probe, locus, map information
- AGI (WebFPC) - FPC fingerprinting/Contig display
- ZmDB - EST sequence information
- TIGR - sequence information
- Gramene