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Table 1 Comprehensive table for comparison of the features of RFLP related software.

From: SNP-RFLPing: restriction enzyme mining for SNPs in genomes

  Input format Output format Type of program Flanking sequence length Graphical display Design of mutagenic primers
SNP-RFLPing 1.rs# IDs, ss# IDs. 2.Many IDs per line (separated by comma symbol). 3.HUGO gene name. 4.Entrez Gene ID. 5.SNP-in-sequences of IUPAC or [dNTP/dNTP] format. 6.Multiple mixed forms: rs#, ss# and sequences are accepted (separated by comma or enter key). 1.On-line and/or email. 2.SNP information provided, e.g., contig position, heterozygosity, function, protein codon. 3.RFLP information, e.g., recognition site, cutting position and strand of restriction enzyme. (visualization of the result). 4.Gene-SNP-RFLP function. (Users can input the gene name and the system can provide all RFLP SNPs of the gene) Web-Server User input Yes Yes
SNPicker [10] 1.sequences only. 1.RFLP information, e.g., recognition site, cutting position and strand of restriction enzyme. 2.no SNP information. Down-load User input Yes Yes
NEBcutter [1] 1.sequences only. 2.no SNP related input. 1.on-line only. 2.no SNP information. Web-Server User input Yes No
SRP Opt [11] 1.sequences only. 2.microbial genome only. 1.not for SNP genotyping. 2.selection of forensic markers. Down-load Not mentioned Yes No
PIRA-PCR Designer [12] 1.sequences only. 1.on-line only. 2.no SNP information. Web-Server User input No Yes
SNP cutter [13] 1.rs# IDs. 2.one ID per line. 3.Specific sequence format (additional software needed). 1.Email only. 2.no SNP information. Web-Server 2000 bp No Yes
SNPselector [14] 1.upload input only. 2.rs# IDs. 3.gene name. 4.genome regions. 5.no sequence input. 1.Email only. 2.no RFLP information. Web-Server 200 bp Yes No
SNP2CAPS [15] 1.alignment sequences. 2.FASTA format only. 1.no auto-mining for RFLP enzyme. Down-load Not mentioned Yes No
In silico software http://www.in-silico.com/restriction/ [16] 1.SNP ID. 2.sequences with SNP or mutation. 3.unaligned or multiple prealigned sequences are accepted. 1.on-line only. 2.SNP position in sequence. 3.RFLP information (including cutting position, selectable function for minimum recognition size, type of enzymes and commercial sources.). 4.multiple SNPs can be compared simultaneously. 5.other useful related tools provided. Web-Server User input Yes Yes