MuSeqBox

a program for Multi-query Sequence Blast output examination

MuSeqBox examines BLAST output, extracts the informative parameters of BLAST hits, and saves them in tabular form. The program can further analyze hit tables to produce subsets of BLAST hits according to user-specified criteria. In particular, BLASTX output may be further analyzed to indicate queries that might potentially be alternatively spliced transcripts (e.g., an extra large segment of insertion or deletion), full-length coding sequences, or contain repeat structures.

Select one of our BLAST output files: Display hits:

Display HSPs:

Print format:

Upload your own BLAST output file (click here for non-GenBank formatted input )
Specify length of Query/Subject ID columns:
Select queries based on the following criteria:
QLen HLen SLen
CovQ % CovS % pid %
Gaps Score Eval
Note: multiple specifications are combined with the logical AND.
Select queries that are globally highly similar to matching subjects:
Parameters required: Pid >= mao <= scv >=
Select queries that potentially encode full-length coding sequences:
Parameters required: ( v5s<= OR v5q<= ) ( v3s<= OR v3q<= ) scv>= qcv>=
Select queries that represent potential alternatively spliced transcripts:

Parameters required:

 indel>= type
Select queries that may contain repeats or align to subject sequences containing repeats:
Parameters required: rps>= src
Send the (text format) output to this email address:
If no options are selected, the top 3 BLAST hits (if any) will be displayed for all queries.

Any comments, please contact vbrendel@iastate.edu

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