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

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)

SNPicker [10]

1.sequences only.

1.RFLP information, e.g., recognition site, cutting position and strand of restriction enzyme.

2.no SNP information.

NEBcutter [1]

1.sequences only.

2.no SNP related input.

1.on-line only.

2.no SNP information.

SRP Opt [11]

1.sequences only.

2.microbial genome only.

1.not for SNP genotyping.

2.selection of forensic markers.

PIRA-PCR Designer [12]

1.sequences only.

1.on-line only.

2.no SNP information.

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.

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.

SNP2CAPS [15]

1.alignment sequences.

2.FASTA format only.

1.no auto-mining for RFLP enzyme.

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.