Exon intron finding tool

This server can accept sequences up to 1 million base pairs 1 Mbp in length. The NetStart server produces neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences. Projector is a program for the comparative, homology based prediction of protein coding genes in mouse and human DNA.

Projector takes the known genes of one DNA sequence and predicts the corresponding genes in an evolutionarily related DNA sequence. Gene Identification. Protea is a software devoted to protein-coding sequences identification. The input is a set of DNA sequences that need not to be aligned. The method takes advantage of the specific substitution pattern of coding sequences together with the consistency of reading frames.

Ecgene is novel gene prediction program that combined genome-based EST clustering and transcript assembly procedures in a coherent fashion andprovides a genome annotaion for alternative splicing. Intron Analysis.

Seq to Fasta. TODO list. Virtual stickIt notes. Web programs. Chromosome lengths. Consensus site finder. Degenerate motif finder. Exon finder. Fusion protein RE. Fusion protein PCR. Genetic distance. Heterozygous InDels.

Invert sequence. List comparison. Microsatellite peaks. Mismatch Tm. Mutagenesis silent. Mutation severity. ORF annotation. Phred score calculation. Protein cleavage fragments. Random sequence. Residue codes etc. Restriction sites. RFLP enzyme picker. Stats decision tree. Novel genomes can be analyzed by GeneMark-ES , an algorithm utilizing models parameterized by unsupervised training.

Notably, GeneMark-ES has a special option for fungal genomes to account for fungal-specific intron organization. Sets of assembled eukaryotic transcripts can be analyzed by the modified GeneMarkS algorithm the set should be large enough to permit self-training.

With this option on, the program will automatically retrieve the SNP information contained in template using GenBank accession or GI as template is required and avoid choosing primers within the SNP regions. If the default "Automatic" setting is selected, the program will automatically select the repeat database using the following rules. If a repeat database is available from the same organism as specified in the "Organism" field by user see above , then that repeat database will be used.

For example, if "Human" is specified, then the human repeat database will be selected. If a repeat database from the same organism is not available, the database from the closest parent of that organism in the taxonomy tree will be selected.

For example, the rodent repeat database will be selected if "Mouse" is specified in "Organism" field. However, no repeat database will be selected if "Gallus gallus" is specified since a repeat database from its taxonomical parents is not available.

This option enables our new graphic view which offers much more details for your template and primers. It will replace the current graphic view in the future. Retrieve recent results Publication Tips for finding specific primers Reset page Save search parameters. It is highly recommended to use refseq accession or GI rather than the raw DNA sequence whenever possible as this allows Primer-BLAST to better identify the template and thus perform better primer specificity checking.

A template is not required if both forward and reverse primers are entered below. The template length is limited to 50, bps. If your template is longer than that, you need to use primer range to limit the length i. Range Help Clear. From To. Forward primer. Reverse primer. Help Optionally enter your pre-designed forward primer. Help Optionally enter your pre-designed reverse primer.

Min Max. Min Opt Max Max T m difference. No preference Primer must span an exon-exon junction Primer may not span an exon-exon junction Help This controls whether the primer should span an exon junction on your mRNA template. Min 5' match Min 3' match Max 3' match.

Enable search for primer pairs specific to the intended PCR template Help With this option on, the program will search the primers against the selected database and determine whether a primer pair can generate a PCR product on any targets in the database based on their matches to the targets and their orientations. Automatic User guided No user guidance Help Primer-blast tries to find target-specific primers by placing candidate primers on unique template regions that are not similar to other targets.

Entrez query optional Help You can use a regular entrez query to limit the database search for primer specificity. Primer must have at least 1 2 3 4 5 6 total mismatches to unintended targets, including at least 1 2 3 4 5 6 mismatches within the last 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 bps at the 3' end.

Help This requires at least one primer for a given primer pair to have the specified number of mismatches to unintended targets.

Ignore targets that have 1 2 3 4 5 6 7 8 9 or more mismatches to the primer. Help This is another parameter that can be used to adjust primer specificity stringecy. Show results in a new window Use new graphic view Help This enables our new graphic display that offers enhanced overview for your template and primers. Note: Parameter values that differ from the default are highlighted in yellow Advanced parameters Primer Pair Specificity Checking Parameters Max number of sequences returned by Blast 10 50 Help Maximum number of database sequences with unique sequence identifier Blast finds for primer-blast to screen for primer pair specificities.

Help The maximum number of PCR targets amplicons to be shown when designing new primers. Help The maximum number of PCR targets amplicons to be shown when checking specificity for pre-designed primers.

Help The maximum number of PCR targets amplicons to be found on any single sequence in the search database. Min Opt Max. Help The number of consecutive Gs and Cs at the 3' end of both the left and right primer.