Sim4 analysis in batch mode

 

cDNA and gDNA alignment, intron-exon structure can be defined thereafter.

Currently, we are only able to handle multiple cDNA sequence against one gDNA sequence alignment

NOTE: Sim4 was designed by Florea L et al.  (Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 1998 8:967-74). 

A web version can be accessed at PBIL (but single sequence analysis)

Alert: Please make sure that your sequence is clean DNA sequence without symbols, such as ":", which can be the product of many sequence assembly programs.  Utility is supplied to clean your FASTA format sequence.

1. Please give the cDNA sequence data file (may contain all the cDNA sequence in FASTA format)

2. Please give the gDNA sequence data file (only one gDNA sequence in FASTA format is allowed)

3. H value: (default 500 for shorter introns, EST above quality cDNA analysis; 1000 could be used for high quality analysis, as full-length cDNA vs high quality gDNA sequence)

4. Remove poly-A tail? (Poly-A tail can cause miss-assigned extra exon)

5. The sim4 results in one file will be delivered to

Email address

choice of output in gzip compressed format:

Your email box accepts message size limit of  per message

If your input data file is from a Mac machine, please be sure to check this box