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BLAST FAQ (Frequently Asked Questions)
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- Which BLAST program should I use?
- How can I search a batch of sequences with BLAST?
- How can I write a program to submit jobs to NCBI's BLAST servers?
- How can I limit my BLAST search based on Organism?
- How can I limit my search to a subset of database sequences?
- Is it possible to search for a motif or pattern with BLAST?
- How do I perform a similarity search with a short peptide/nucleotide sequence?
- Can I use BLAST to compare two or more sequences in a multiple sequence alignment?
- What is the Expect (E) value?
- What is low-complexity sequence?
- Other Molecular Biology Resources
- Why do I get the "No Significant similarity found" error message?
- Why does my search timeout on the BLAST servers?
- Why do I get the error message "ERROR: BLASTSetUpSearch: Unable to calculate Karlin-Altschul params, check query sequence"?
- Why do I get the error message "ERROR: Blast: No Valid Letters to be indexed?"
- Why do I see a string of "X"s (or "N") in my query sequence that I did not put there?
- I have heard that I will be penalized if I send a large number of sequences to the servers?
Q: Which BLAST program should I use?You have
many choices to make between different BLAST programs and
databases. Some of these choices are better for answering
some questions then others. We have created a selection
chart to help you make the decision of BLAST program for
the question you are asking. This is the "BLAST
Program Selection Guide".
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