This is BLAT program installation at CBSU. This program currently runs on our Windows cluster as x64 application using Subsystem for UNIX-based applications (SUA).  For options and program documentaion please refer to BLAT FAQ and BLAT program specifications. Please send questions/comments regarding this BLAT installation to cbsu@cac.cornell.edu. Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page. NOTE: Do not use "Back" button in your browser to reaccess this page after submitting. Use menu on the left instead.

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E-mail:   (only guests need to use this field, registered users should log in)

Job name:   (please, no spaces, special characters etc., uderscore is OK)

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Query  file (Required):   uploadcopypaste

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Choose database for BLAT: from listcopyupload

 Run: Batch Real-time    Cluster: 
( Show timeout info )

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Options:

dna prot dnax Database type. Type is one of: dna - DNA sequence; prot - protein sequence; dnax - DNA sequence translated in six frames to protein dna rna prot dnax rnax Query type. Type is one of: dna - DNA sequence; rna - RNA sequence; prot - protein sequence; dnax - DNA sequence translated in six frames to protein; rnax - DNA sequence translated in three frames to protein -tileSize=N. Sets the size of match that triggers an alignment. Usually between 8 and 12. Default is 11 for DNA and 5 for protein. -stepSize=N. Spacing between tiles. Default is tileSize. -oneOff=N If set to 1 this allows one mismatch in tile and still triggers an alignments. Default is 0. -minMatch=N sets the number of tile matches. Usually set from 2 to 4 Default is 2 for nucleotide, 1 for protein. -minScore=N sets minimum score. This is the matches minus the mismatches minus some sort of gap penalty. Default is 30 -minIdentity=N Sets minimum sequence identity (in percent). Default is 90 for nucleotide searches, 25 for protein or translated protein searches. -maxGap=N sets the size of maximum gap between tiles in a clump. Usually set from 0 to 3. Default is 2. Only relevent for minMatch > 1. -noHead suppress .psl header (so it's just a tab-separated file)  N= -makeOoc=N.ooc Make overused tile file. Target needs to be complete genome. -repMatch=N sets the number of repetitions of a tile allowed before it is marked as overused. Typically this is 256 for tileSize 12, 1024 for tile size 11, 4096 for tile size 10. Default is 1024. Typically only comes into play with makeOoc. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate. no mask lower upper -mask=type Mask out repeats. Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas are ignored entirely in protein or translated searches. Types are: lower - mask out lower cased sequence; upper - mask out upper cased sequence. no mask lower upper -qMask=type Mask out repeats in query sequence. Similar to -mask above but for query rather than target sequence. no mask lower upper out file.out -repeats=type Type is same as mask types above. Repeat bases will not be masked in any way, but matches in repeat areas will be reported -minRepDivergence=NN - minimum percent divergence of repeats to allow them to be unmasked. Default is 15. Only relevant for masking using RepeatMasker .out files. -dots=N Output dot every N sequences to show program's progress -trimT Trim leading poly-T -noTrimA Don't trim trailing poly-A -trimHardA Remove poly-A tail from qSize as well as alignments in psl output -fastMap Run for fast DNA/DNA remapping - not allowing introns, requiring high %ID psl pslx axt maf sim4 wublast blast blast8 blast9 -out=type Controls output file format. Type is one of: psl - Default. Tab separated format, no sequence; pslx - Tab separated format with sequence; axt - blastz-associated axt format; maf - multiz-associated maf format; sim4 - similar to sim4 format; wublast - similar to wublast format; blast - similar to NCBI blast format; blast8- NCBI blast tabular format; blast9 - NCBI blast tabular format with comments -fine For high quality mRNAs look harder for small initial and terminal exons. Not recommended for ESTs -maxIntron=N Sets maximum intron size. Default is 750000 -extendThroughN - Allows extension of alignment through large blocks of N's