To construct a bicistronic expression vector pcDNA3.1AB controlled by two CMV promoters,pcDNA3.1A and pcDNA3.1B were constructed first by reforming the MCS of pcDNA3.1(+).The PCR product of-PCMV-MCS-BGHpolyA-from pcDNA3.1A was inserted into pcDNA3.1B to form pcDNA3.1AB.DsRed gene and EGFP gene were inserted into pcDNA3.1AB to construct pcDNA-DsRed,pcDNA-EGFP and pcDNA-DsRed-EGFP.The recombinants were transfected and transiently expressed in COS-7 cells and detected by fluorescence microscope. DsRed and EGFP were coexpress in pcDNA-EGFP-DsRed, and the fluorescence intensity had no significant deviation.The fluorescence intensity was similar between monocistronic and bicistronic vectors.The successful construction and expression of pcDNA3.1AB lay foundation for the advance research of gene expression and bigem DNA vaccine.

In this study, the four repeats of chicken CCK-33 gene were successfully amplified by PCR. The 4CCK-33 fragment was inserted into plasmid pBCX to obtain recombinant plasmid pBCX-4CCK33. The recombinant plasmid was conducted into E.coli BL-21 to induce 4CCK-33 gene fusion expression. The fusion protein band with molecular weight of 53ku was detected on the SDS-PAGE gel; the peak expession level of fusion proteins occupied 30.08% of the total bacterial protein. What’s more, most fusion proteins were soluble. Western blotting showed that the expression products can specifically reacted with the antisera of CCK-8. The purified fusion proteins were used as antigen to prepare oil-emulsion vaccines, and the laying hens were immunized. ELISA results indicated that the vaccine can resulted in immune response. 82-day old pigs were inactively immunized with yolk powder containing CCK antibodies. The results showed that pigs fed diets with dried yolk powder containing CCK antibodies at the level of 100 g/t showed significant higher average daily gain and feed intake than the control group, with increase by 6.64% and 8% respectively.

The full-length coding region of PEA gene was amplified by PCR method from genomic DNA of ATCC27853 Strain of Pseudomonas aeruginosa . The PEA gene was inserted into eucaryotic expression vector pcDNA3.1A to constructe plasmid expression vector pcDNA3.1/PEA . The recombinant plasmids were transfected into HEK 293T cells to be expressed by calcium phosphate mediation. The results showed that cloned PEA gene shared 99% alignment with standard strain PA103. The PEA gene product was detected in the medium with Western blot, which indicated that the PEA gene with original signal peptide could be expressed with secretary form in eucaryotic cells. These lay the foundation for the further research of PEA-based immunotoxin , vaccine adjuvant and vaccine vector.

CRS-PCR Polymorphisms of GHR Gene and Its Relationship with Milk Production Traits in Chinese Holstein Cows

Three pairs specificity primers was designed for amplification of adiponectin gene in geese according to the known sequence of chicken, duck , etc. The sequence of adiponectin gene in geese was obtained by PCR amplification and splicing. It contains two exons and one intron. The coding sequence is 738 bp and codes 245 amino acids. The coding sequence and the corresponding protein of geese adiponectin shares the highest homology with duck′s, which are 94.85% and 95.51% respectively, then was chicken’s, the lowest homology with mammals’. The predicted molecular weight (MW) and isoelectric point (pI) are 26603.3 Da and 5.19 respectively, which are highly similar to the above animals′. Reverse transcription-PCR revealed that geese adiponectin mRNA displayed high expression levels in skeletal muscle, fat tissue, heart and stomachus muscularis ,middle expression in small intestine, stomachus glandularis, kidney and lung, and weak expression in liver, spleen, ovaries and diencephalons. The result will be helpful for further studying the function and mechanism of the adiponectin gene in geese.

The applicability of 14 pairs microsatellite primers of blue peafowl and green peafowl to white peafowl population was analyzed in the present paper, and the results showed all 14 pairs of microsatellite primers could produce specific allele patterns. A mean of 1.71 alleles was found for each locus. Seven pairs were highly polymorphic, MCW0080 and MCW0098 were ideal markers for peafowl. Genetic diversity analysis of three peafowl populations demonstrated that the heterozygosity and the genetic diversity of these peafowl populations were very low, the expected heterozygosity of white peafowls, green peafowl and blue peafowl population were 0.2579, 0.2482 and 0.2744, respectively. Genetic differentiation index (FST) of these populations was 9.7% and there was significant genetic differentiation among three populations(P<0.001). The result showed that white peafowl has a closer relationship with blue peafowl than with green peafowl, Reynolds' genetic distance and gene flow between the two populations were 0.0295 and 8.6112, respectively. The results of this study support that white peafowl is not subspecies but a line belonging to blue peafowl.

17 distinguished loci were screened out of 77 microsatellite to check the genomic DNA of three varieties of, including differential locus of O.aureus UNH636, UNH117, UNH172, UNH738, UNH878, UNH896, O. niloticus UNH913, UNH907, UNH222, UNH980, UNH880 and O. mossambicu UNH876, UNH899, UNH853, UNH932, UNH933, UNH773. Anyone of 17 loci amplified particular bands of one strain of tilapia. So these loci can distinguish one tilapia from the other. The genetic structure and the phylogenetic relationships of three tilapias were analysis by using this 17 microsatellite loci, there were totally 142 alleles of these microsatellite loci, and the average number of alleles was 8.35. Additionally, a clustering analysis was made based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using UPGMA method. The results showed that, the mean value of observed heterozygosity of O. aureus, O. niloticus and O. mossambicu was 0.0941, 0.5490, 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230, 0.2608, and the polymorphism information content (PIC) was 0.1089, 0.7230 and 0.2608 respectively. It indicated that, the genetic diversity of O. niloticus was highest and O.aureus was lowest. The phylogenetic tree shows that the genetic relation between O.aureus and O. mossambicu is closer than their relationship with O. niloticus, which was similar to others reports.

In this study, SSR analysis was performed on five Secale species, four Triticum species, and a Triticale with branch-like using 102 pairs of microsatellite primers. A 387bp specific DNA fragment FZ387 (Accession No. EF179137), was obtained from Triticale with branched-like by primer Xgwm614; however no amplification result revealed in Secale. The result of sequence comparison revealed this sequence had 94% and 95% similarity with a part of Gypsy Ty3-LTR-retrotransposon fatima in T. monoccocum (AY485644) and T. turgidum（AY494981）, respectively. Based on the conservative region of this sequence, a pair of specific PCR primers, FaF and FaR, was designed. The result of amplification by Xgwm614F and FaR revealed that a specific DNA band of about 350 bp (designation as A350) was obtained from species containing A chromosomes; however, this segment was not appeared in materials not contain A chromosome. Chromosome map was performed on Landon Chinese Spring substitution lines and the result suggested that this segment was located on both long and short arms of all A chromosomes. Also the result of amplification by FaF and Xgwm614R appeared that a specific DNA band with about 350bp (designation as AB350) was obtained from materials containing A or/and B chromosomes; nevertheless this band was not revealed in materials not contain A and B genomes. Using the two pairs of primers, the result of amplification on relative species of Triticum revealed only A350 and AB350 in CS. The result of sequence comparison and variation of SSR primers binding regions of FZ387 indicated that significant diversity may existed in the internal sequence of this fatima element between genus and similarities within genus. Meanwhile, A350 and AB350 could be used as molecular markers for the detection of A and AB chromosomes.

Abstract: Protein kinase plays an important role in stress signal transduction in plant. One full-length cDNA encoding a CIPKs homologue was isolated from maize through in silico cloning and named as ZmCIPK1. The predicted ZmCIPK1 protein has 465 amino acids with an estimated molecular mass of 51.98 KD and an isoelectric point of 6.92. The putative kinase catalytic domain of ZmCIPK1 contains the 11 subdomains that are typical in protein kinase. The conserved 24-amino acid motif within the C-terminal non-kinase region of the CIPKs is also found in ZmCIPK1. RT-PCR analysis indicated that ZmCIPK1 expression was up-regulated obviously by mannitol, salt, ABA and low-temperature in young leaves and kept high level during 24 hours. These results demonstrate that ZmCIPK1 is a novel CIPK gene and responds to multiple abiotic signals in maize. key words: maize; CIPK; abiotic stress

The pokeweed antiviral protein (PAP) gene was transferred into the cotyledons of mustard (Brassica Juncea Coss.) mediated by Agrobacterium tumefaciens. Using PCR technology to analyse 40 anti-kanamycin plants, 29 positive plants were obtained. The result of Southern blot analysis was that there were single copy or double copies of transgene in the transgenic plants. The result of Northern blot analysis was that the PAP gene was normally expressed in transgenic plants. The results of transgenic plants inoculated with virus TuMV showed that the transgenic plants were more resistant to TuMV than non-transgenic plants.

Abstract: This study was aimed to compare the contents of endogenous cytokine (ZRs、DHZRs、iPAs ) and auxin (IAA) in decussate and alternative maize by the ELISA method .Two sets of near isogenic lines of 8701d, 8701D and H4d, H4D were used in these examinations. In this study, the results showed that the maize with different phyllotary leaf had same level of endogenous cytokine (ZRs、DHZRs、iPAs ) and auxin in mature pollen ,different development leaf and young embryo. However，the contents of above cytokine in immature male spikes from decussate plants and SAMs were great higher than that in isogenic alternative maize. At the same time, there was no significant difference in the level of IAA among them. Further analysis indicated that the value of CTK/IAA in decussate maize was not only dominant higher than in alternative maize, but also was increased accompanied with phyllotary changes from alternative to decussate. Taken together, we can draw a conclusion that there is close relativity between the decussate phenotype and the level of SAM cytokines. The stabilization and change of CTK/IAA is an important factor which regulates phyllotary development.The producing of decussate mutant is relative to the change of endogenous hormone content in growthing tissue.

The crystal consisting of Cry7Ba1 crystal protein from Bacillus thuringiensis could be dissolved only at pH values of >11.5, and did not exhibit toxicity while it was not dissolved. In this study, the C-terminal half of Cry7Ba1 were replaced by that of Cry1C and Cry1Ac, respectively. The results indicated that, when the C-terminal half of Cry7Ba1 was substituted, the crystal formed by the recombinant crystal proteins could be dissolved in alkaline buffer (pH9.5) as that of Cry1Ac and Cry1C did, and the toxicity has not be changed. These data suggested that the property of insolubility of Cry7Ba1 crystal was associated with the structure of C-terminal half. This research could improve the solubility through swapping the C-terminal half of Cry7Ba1, and supplied possibility for the crystal protein biocontrol application.

Zwittermicin A (ZwA) is a novel antibiotic which shows diverse inhibitory activity against a broad target of plant pathogens. It was first discovered from Bacillus cereus strain UW85, and zmaR is its resistant gene. Since we have already got the entire genome of Bacillus thuringiensis strain YBT-1520, which is also produce ZwA, we analyze the synthesis gene cluster of ZwA in strain YBT-1520 and found that at the downsteam of the gene cluster there was some sequence highly similar with ABC transporter（zwa-FEG). When the zwa-FEG was transferred to E. coli DH10B, it could obtain the resistant ability to ZwA. When zwa-FEG gene was transferred to ZwA-producing strain UW85, the production of ZwA was improved. It suggested that zwa-EFG is a cluster coding ABC transporter, and it could affect the resistance to ZwA.

The industrial strain BIB0830 of Streptomyces thermotolerans can produce acetyl-isovaleryl tylosin(AIV) by bioconversion using tylosin as a processor. Recombinant plasmid pBIB425 containing structural gene of acyB1-B2, pBIB304 containing up-mutant promoter of ermE（ermEp* ）and structural gene of ermE, were derived from pIJ8600. The recombinant strain BIB425, BIB304 and BIB308 were obtained by introducing pBIB425, pBIB304 and pBIB308 containing disruption cassette of nsdA gene (stored by lab) respectively into the industrial strain BIB0830 through intergeneric conjugal transfer. After PCR analysis, they were confirmed to be the positive clones. Compared with the start strain BIB0830, in the level of flask, the bioconversion abilities of tylosin to acetyl-isovaleryl tylosin (AIV) of recombiant BIB425 and BIB308 increased 14% and 22%, respectively .The BIB304 was not affected.

Plant expression vector pBI121/Ω4A/aac was constructed by cloning of aac gene which can quench the quorum-sensing of Ralstonia solanacearum. The aac gene was transferred into tobacco mediated by Agrobacterium tumefaciens. Under Kanamycin selection pressure, fifty-seven resistant lines were obtained. PCR, RT-PCR analysis indicated that aac gene had been integrated in tobacco genome and translated. Inoculation testing showed that the disease index of transgenic tobacco was reduced by 51 in greenhouse after 16 days of inoculation, 56.5 percentage points down from the contrast.

Setosphearia turcica is the causal agent of northern leaf blight of corn. We obtained a homologous fragment of Gβ gene from S. turcica, which was named as Stgb-1 and similar to homologus regions of other fungal Gβ genes. The 3’ cDNA end of Stgb-1 showed a 3’UTR containing 136 bp and a poly(A) tail containing nine A’s. Based on its high identity with CGB-1 in Cochliobolus heterostrophus, we designed specific primers which were corresponding to CGB-1 ORF and obtained succesfully the full length Stgb-1 ORF. It was 1056 bp and encoded 351 amino acid residues. The whole ORF was devided into 5 exons and 4 introns. The predicted protein sequence shared a high degree of sequence identity with Gβ protein from C. heterostrophus (100%), Cryphonectria parasitica (80%), Aspergillus fumigatus(81%). The sequence had been deposited in the GenBank/EBI Data Libraries under Accession No. EF407555. We used pET system to express Stgb-1. Results of SDS-PAGE and Western blotting showed that the recombinant protein with the calculated molecular mass of 40 kDa was expressed in E.coli. In conclusion, we had successfully cloned Gβ subunit gene of S. turcica and got the His-tag recombinant protein.

Lactobacillus paracasei MA3, harboring two natural plasmids, was isolated from fresh milk using selective medium SL. In order to obtain the complete sequence, the unknown small plasmid pMA3 was digested with ScaI and ligated with vector pBK-CMV. The complete sequence of pMA3 revealed to be 5809bp in length with GC content of 39.54%. The computer analysis revealed that pMA3 harbored four ORFs, one of them designated Rep3, which is replication initiation protein. Sequence analysis results determined the highly homologous similarity of Rep protein and the tandem direct repeats, which demonstrated that pMA3 belongs to the pUCL-287 subfamily of theta-type replicons. This plasmid has been deposited in GenBank under Accession No.EU255257.This research has made a basis for developing the food-grade expressing vector with independent intellectual property rights.

The expressed protein had been purified and analyzed. at the same time, The inductive conditions used lactose as inducer for the flask-shaking of E.coli BL21-pET-hBD3-Bra had been optimized. The purified hBD3-Bra（recombinant protein of human β defensin 3 and des-pGlu-brazzein ）had weak antimicrobial activity, but shew little sweet . After digested by thrombin and purified by affinity column, the recombinant hBD3 had high antimicrobial activity and the natural des-pGlu1-Brazzein was 600 times sweeter than that of sucrose. The Influences of three factors which were lactose concentration, induction time and temperature on growth of strain and on yield of hBD3-Bra was analyzed in detail. The result indicated that higher lactose concentration inhibit the growth of strains（P<0.01）, but had little effect on expression of target protein among 0.5%-5%(P>0.05), Biomass would be improved as time passed（P<0.01），but the yield of target protein didn’t increase obviously simultaneously（P>0.05). Temperature was a important factor effect on growth of strain and expression of target protein（P<0.01）. Further analysis shew that the best temperature for growth was 30℃-32℃ and for expression was 30℃. Lactose as inducer was as good as IPTG as inducer (P>0.05).

To investigate the synergism of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) chitinase with insect pathogens for pest control, the chitinase A (chiA) gene was amplified from the AcMNPV genome by PCR and expressed in E. coli BL21 and Spodoptera frugiperda cell line Sf-9 respectively. The results of SDS-PAGE showed that chiA gene could be expressed as a 60 kDa protein in both E. coli and Sf-9 successfully. When the fifth instar larvae of Helicoverpa armigera were fed with the expressed product of chiA gene, the perforations on the peritrophic membrane (PM) were observed by the scanning electron microscope (SEM). When the expressed product of chiA gene was mixed with Bt and with Mamestra brassica nuclear polyhedrosis virus (MbNPV) fed to larvae of Helicoverpa armigera respectively. Then bioassay indicated that when compared with their corresponding controls, the LT50 of Helicoverpa armigera larvae fed by a mixture of Bt Cry2Ac protein and expressed product of chiA gene in E. coli and in Sf-9 cells were shortened 17.8 and 20.6 hours, with rates of enhancement were 33.4% and 54.5%, respectively. Another LT50 of Helicoverpa armigera larvae fed with MbNPV and expressed product of chiA gene in E. coli and in Sf-9 cells were shortened 16.6 and 22.4 hours, respectively. These results suggested that AcMNPV Chitinase may enhance insecticidal activity of Bt and NPV for pest control.

Forty-nine isolates of Trichoderma were collected and isolated from spawn and fruiting body of edible fungi. They were identified based on morphological taxonomy proposed by Gams & bissett (1998) and ITS analysis. The results showed that Trichoderma species associated with cultivated edible fungi from Fujian and Zhejiang of China were dominated by T. harzianum and T. longibrachiatum , but T. atroviride and T. asperellum were rare. Species of Trichoderma varied with collection locality and mushroom species concerned. Trichoderma isolated from spawn of Lentinula edodes was dominated by T. harzianum in Qingyuan country of Zhejiang province.Trichoderma isolated from spawn of Pleurotus eryngii was dominated by T. asperellum in Guangzhou, while that isolated from spawn of cultivated lentinula edodes was dominated by T. atroviride in Pucheng of Fujian province. The result of morphological identification and that of ITS analysis was approximately coincident

Twelve infectious bronchitis virus isolates obtained from commercial suspect chicken flocks in China between 2005 and 2006 were characterized by genotyping and investigation of biological characteristics. Evidence suggested that eleven of the twelve infectious bronchitis virus belonged to the LX4-type and CK/CH/LSC/99I-type. CK/CH/LSD/05I—an IBV variant, which was identified by the phylogenic analysis, BLAST searches of the entire S1 gene and the vaccination-challenge test. Virulence studies indicated that there are not obviously kidney pathological changes on chickens, and the rate of recovery of the virus in the kidney and trachea is 20﹪ and 100﹪, respectively, post-inoculation. Thus CK/CH/LSD/05I was unlike the nephropathogenic IBV isolates found in China, however, it exhibited an affinity for the respiratory tract. Additionally, sufficient respiratory protection was not provided by the commercial vaccine H120 and three heterologous strains against CK/CH/LSD/05I challenge. It was showed that CK/CH/LSD/05I may be a variant of IBV.

Chinese cabbage - head cabbage alien addition lines were middle materials to genetic improvement in Chinese cabbage using good genes of head cabbage, and have important value in genetic theory research and breeding practice. In this study, the mosomic addition line named CO-4-1(Chinese cabbage with 4# chromosome from cabbage) from the progenies of AAC(2n=29)×AA(2n=20)was obtained by cytology identification,observed and investigated the PMC meiosis behavior and the field character of the plants.The obtained alien addition lines would be used to explore the relation between A and C genomes, transmitting good genes to Chinese cabbage, genome directionally widening genetic background of Chinese cabbage and increasing genetic diversity.

A BC1F5 population consisting of 202 lines developed from Xieqingzao B//Xieqingzao B/Dongxiang wild rice was tested for yield traits in two years in the same trial site. A total of 23 QTLs for yield traits were detected using a linkage map consisting of 149 markers. The numbers of QTLs detected for individual traits were two for the number of panicle per plant (NP), four for the number of filled grains per panicle (NFGP), six for the total number of spikelets per panicle (TNSP), five for spikelet fertility (SF), four for 1000-grain weight (TGWT) and two for grain yield per plant (GYD). Nine of the QTLs had the enhancing alleles from the Dongxiang wild rice, including two for NP, one for NFGP, five for TNSP and one for TGWT. Six of them were located in intervals where QTLs for yield traits have been reported in other studies using interspecies populations of rice. The 23 QTLs were distributed in all the 12 rice chromosomes except chromosome 11. Eighteen of the QTLs were located in eight clusters. The enhancing alleles were from Xieqingzao B in four clusters and from the Dongxiang wild rice in two clusters, while the allelic direction in the remaining clusters varied for different traits. Work is underway to construct populations for fine mapping the QTLs.

Levels of genetic diversity within and among 56 germplasm of Pyrus were analyzed using SSR markers. 40 bands were amplified by six informative and reliable prmiers screened, of which 38 (95% ) were polymorphic, with an average of 6.3 alleles per locus. Nei’s gene diversity index ranged from 0.0354 to 0.491 with an average of 0.1964 , effective number of alleles range from1.0367 to 1.9648 with an average of 1.2958. Genetic diversity difference among tested pear cultivars was relatively low based on Shannon index (0.3256). 44 pear cultivars could be distinguished by SSR markers except the mutant cultivars. UPGMA cluster analysis was performed with soft NTYSIS-pc2.01, the clades formed including four populations at the dice coefficient of 0.71. Pyrus bretschneideri Rehd., P. ussuriensis Maxim. and P. pyrifolia Nakai. originating in China interveined each other and could not form group independently .

The genetic diversity and relationship of 10 P.ternta of JingZhou with different leaf shape were analyzed by SRAP. The DNAS of 10 P.ternta of JingZhou were tested with SRAP using 40 primer pairs and 39 primer pairs showed polymorphism. A total of 632 polymorphic bands were obtained and there were 16.2 polymorphic bands of per primer pairs. The SRAP based genetic similarity ranged 0.105~0.978, UPGMA cluster analysis based on SRAP molecular markers data divided 10 different leaf shape into five groups: the result of UPGMA divided trifoliate P.ternta of JingZhou and quinquefoliolate P.ternta of JingZhou into two group. There are four small group in trifoliate P.ternta of JingZhou:Ⅰ: auricular leaf、cuspate leaf、rounded leaf、terrace leaf、thin peony leaf and peony leaf；Ⅱ: auricular leaf with emargination；Ⅲ: wide angustifoliate；Ⅳ: angustifoliate. This study provided an new marker system for P.ternta variety identification and genetic research, which would be helped to reveal the genetic background and relationship of P.ternta germplasms .

To get the epitope site of NDV-HN protein which may be identified with mAb 1E5, monoclonal antibody of NDV-HN protein was used to screen the phage display random 7-peptides. The positive clonies were identified by indirect ELISA and competitive ELISA. 4 groups of 7-peptides sequence were got These sequences were located at the residue 388~395 aa of NDV-HN protein.The mutual sequence L * * * PNT is the framework structure. This epitope site is different with former reports, It may be another useful epitope site of NDV-HN protein.

The triose phosphate translocator(TPT)cDNA of full length was amplified by RT-PCR. Sequence analysis indicated that the full length cDNA fragment was showing 99.9％ homology to the sequence reported before．Only one base is different．The sense expression vector with TPT full length cDNA under the control of CaMV 35S promoter was constructed and were transformed into tobacco by leaf disc transformation．The transformed tobaccos were identified by PCR and Southern blotting analysis．

Baculovirus is an specific pathogen for insect, particularly for the Lepidoptera insects. Since the 1980s, the baculovirus was successfully developed as vector for foreign gene expression, it was extensively applied for recombinant protein production. In recent years, lots of interesting studies were done by developing baculovirus for application in new fields, including protein display system, transfer vector for mammalian cells, immobilization of foreign protein, as well as specific materials for nanobiotechnology.

Resources on the Internet of RNA were reviewed by Chen et al. in 2000. However, since 2000, a remarkable progress has been made on research of RNA. Non-coding RNA (ncRNA)，which is not translated into a protein，becomes one of the hottest topics in modern molecular biology. We summarized that new progress on internet resources of sequence, structure, web tool and software related to non-coding RNA from 2000 to end of May, 2007. 1) We found over 50 sequence databases of ncRNA on the Internet. About 30 million sequences were collected in those databases. Integrated databases, e.g. NONCODE and RNAdb, mainly provide original sequence information of various types of non-coding ncRNA. Specialized databases, such as miBase, miRNAMAP and HuSiDa, offer not only sequences but functions, structure, reference etc. of a certain type of ncRNA. 2) We searched 13 structure databases of ncRNA and about 1,200 crystal structures and hundreds of forecasted structures. NDB and PDB supply information on crystal structure of ncRNA measured by NMR spectroscopy and by X-ray crystallography. Rfam and CRW contain secondary structure of ncRNA predicted by comparative sequence analysis. SCOR, RAG and MeRNA offer specialized information such as structure classification, topological structure, and special structure. 3) About 30 software tools were available on the Internet for ncRNA analysis. Mfold was developed to predict secondary structure of RNA. miRanda, TargetScan, PictTar and RNAhybrid are used for predicting miRNA’s target gene. Amibion, Invivoge and Whitehead offer the function of siRNA design. PHYLIP, MEGA, PAUP* are famous software for analysis of phylogenetics. In addition, we discussed the bioinformatic works we need do in near future, i.e. to develop 1) a search engine of ncRNA, 2) a new approach for predicting secondary structure of ncRNA, and 3) a method to mine the potential information of sequence and structure of ncRNA.