Program for mapping a whole set of mRNAs/ESTs to a chromosome sequence. For example, 11,000 sequences of full mRNAs from NCBI reference set were mapped to 52-MB unmasked Y chromosome fragment in about 18-25 min, depending on computer memory size. EstMap takes into account statistical features of splice sites for more accurate mapping.
EstMap is part of FGENESH++C genome annotation pipeline, where it maps RefSeq sequences to a query genome at very early stages of annotation.
Example of an output of the EstMap program:
L:49476872 Sequence chr22 vs. 2 Base sequences [/home/apache/tmp/RrdFeT.rnamap]. [DD] Sequence: 1( 1), S: 26.989, L: 360 AA704607 zj19g11.s1 Soares_fetal_liver_spleen_1NFLS_S1 Homo sapiens cDNA clone 1 nnnnnnnnnnnnnnn(..)ttttttttttttttt?[GAAGGTTTCAAATATACTTTATTT ...............(..)............... |||||||||||||0|||||||||| 1 ---------------(..)--------------- GAAGGTTTCAAATGTACTTTATTT 33914973 CTTCAATAAT]gtcatatcttttttt(..)ccacgcccggctaat[TCTTAATGGGCACA |||||||||| ...............(..)............... ||||||||||0||| 25 CTTCAATAAT gcc------------(..)------------ata TCTTAATGGGTACA 33915177 CAGTGCTTTCACTTGGCATCAATCATGAGCTGTTTTTTAAACAATTCGGTATTACACCAG |||||||||0|0|||||||||||0|||||||||||||||||||||||00||||||||||| 55 CAGTGCTTTAATTTGGCATCAATTATGAGCTGTTTTTTAAACAATTCATTATTACACCAG 33915237 CTGGAATGATCACTGATctatccgTCCT-------TTTGGGGTGGCTCAGCTAACAGGGG ||||0|||||0||||||.......||||.......||||||||00|||0||0|||||||| 115 CTGGGATGATTACTGAT-------TCCTccattccTTTGGGGTAACTCTGCCAACAGGGG 33915290 ATGGGTTCCATTCCATTTCGATTTGTGTTGCTACACTTGTCCATACAGCAGTACAGAAAG |00||||||||||0|||0|||0|||||||||||||00|||||||00|0||0||||||||| 168 ACAGGTTCCATTCTATTCCGACTTGTGTTGCTACATATGTCCATGTAACAATACAGAAAG 33915350 TGGCTCCACTAGCTAATACAGCATTACCATATCTGTCATGAAAATCAGGTGTACCTTTCT ||||||||||||||||||||||||||||0|||0|||||||||||||||||||||0||||| 228 TGGCTCCACTAGCTAATACAGCATTACCGTATTTGTCATGAAAATCAGGTGTACGTTTCT 33915410 GGTGGCTCTGCCTTGCCATTGTTTGCTGAATGCTTCGAACTTGGAGACGA]?cttgagtg |||||||||||00||||||||||||||||||||||||||||||||||||| ........ 288 GGTGGCTCTGCTCTGCCATTGTTTGCTGAATGCTTCGAACTTGGAGACGA tttagtgc 33915468 tgttttt(..)nnnnnnnnnnnnnnn .......(..)............... 346 gcttttg(..)---------------