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Cloning and expression of the cDNA for human antithrombin III.

A partial cDNA clone for human antithrombin III (ATIII) was obtained by screening a cDNA library prepared from size fractionated liver RNA with a pool of eight 16-base long synthetic DNA fragments whose sequence was determined from protein sequence data. A fragment of the partial cDNA clone was used to enrich RNA for ATIII messages, and cDNA clones encoding the entire ATIII structural gene were identified. The complete nucleotide and predicted amino acid sequences of human ATIII and its 32 residue signal peptide are reported, and provide further opportunity to compare the ATIII primary structure with corresponding regions from homologous proteins, alpha 1-antitrypsin and ovalbumin. Plasmids in which the structural genes for mature and pre-ATIII were linked to the E. coli trp promoter-operator support the synthesis of human antithrombin III and pre-antithrombin III in bacteria.

Amino Acid Sequence↗

Renal metabolism of the beta-subunit of human choriogonadotropin in the rat.

We analyzed the immunoreactive renal metabolites of the beta-subunit moieties of unlabeled highly purified hCG, hCG beta, and desialylated hCG (as-hCG) in rats by RIA and Sephadex G-100 chromatography. Infusions of hCG beta, as-hCG, or intact hCG resulted in accumulation in the kidney of a large quantity of small mol wt peptides lacking the immunological determinants of the carboxy-terminal peptide (CTP) of the beta-subunit. In the case of as-hCG, renal accumulation of these beta-core fragments was greatly enhanced when as-hCG binding to hepatic galactose receptors was inhibited by infusion of as-fetuin. The beta-core fragments in kidney had the same immunological and G-100 chromatographic characteristics as beta-core fragments in liver, suggesting similar intracellular catabolic mechanisms in these tissues. The kinetics of beta-core fragment turnover in kidney were studied after injection of hCG beta, which is cleared from the circulation within 1 h. Loss of beta CTP immunoreactivity was the initial event in hCB beta catabolism by the kidney; most of this process occurred between 7 and 30 min after injection. This was followed by a gradual reduction of the size of accumulated hCG beta metabolites over the next 60 min. The beta-core fragments that accumulated had a Kav of approximately 0.57 and a very slow degradation rate over the next 5 h (half-life greater than 6 h). Chromatographic analysis of urine obtained 6 h after beginning a continuous infusion of hCG, hCG beta, or as-hCG displayed in each case a major peak corresponding to the infused molecule, apparently intact, and a minor peak of beta CTP immunoreactivity of small mol wt. Relative to the beta CTP fragments apparent in urine, there were few beta-core fragments. These data indicate that separate fates exist for immunoreactive fragments generated by hCG beta metabolism in the rat kidney. One appears to be intracellular and similar to the liver pathway of as-hCG degradation in that it leads to the formation of long-lived beta-core fragments. The other takes place within ready access to the urinary compartment and leads to the accumulation in urine of beta-CTP fragments.

Animals↗

Binding of 1,25-dihydroxyvitamin D3 receptors to the 5'-flanking region of the bovine parathyroid hormone gene.

To further define the binding site for receptors for 1,25(OH)2D3 (VDR) in the bovine PTH gene and to study the interactions of transcription factors with VDR, Southwestern and gel shift assays were used. Data from the former indicated binding of VDR to DNA fragments spanning the regions -451 to -348 bp and -668 to -452 bp. Studies using gel shift assays confirmed binding to the -451 to -348 bp fragment and specificity was shown by using excess concentrations of unlabelled -451 to -348 bp fragment to compete for binding, whereas excess unlabelled -347 to +50 bp did not compete. Binding was also observed with the -668 to -452 bp fragment but excess concentrations of unlabelled -668 to -452 or -451 to -348 bp fragments did not compete for binding to radiolabelled fragments. These data indicate the presence of two binding domains within this region; the upstream element having a lower affinity for VDR than the downstream element. In addition, there was no interaction between VDR and consensus sequences for AP1, AP2, AP3 and SP1. The putative vitamin D3 response element (VDRE) contains two similar hexameric steroid response element-like half-sites placed as AGGTCA-related direct repeats. The upstream repeat is at -461 to -456 bp and the downstream element is at -449 to -444 bp. The presence of these half-sites is consistent with our experimental data in which cleavage with SspI at -452 bp resulted in two DNA fragments which bound VDR.

Animals↗

Mapping and DNA sequence analysis of the cytomegalovirus transforming domain III (mtrIII).

The transforming activity of XbaI fragment E (map units 0.685-0.770) of human cytomegalovirus Towne strain was originally localized in two terminal segments, 3 kb XbaI-BamHI EM (mtrII) and 7.5 kb BamHI-XbaI EJ (mtrIII). Three immediate-early genes, IE1 to IE3, are located in the same region (map unit 0.685-0.770), and IE1 is located in the EJ fragment. IE1 protein increases chromatin transcriptional activity and causes alteration in chromatin conformation. In this study, we have investigated the potential transforming activity of IE1, IE1 plus its promoter-regulatory region (IE P/R), and the remaining fragment of EJ after deletion of IE1 plus IE P/R. Our results clearly demonstrate that IE1 or IE1 plus IE P/R is not involved in transformation, and that the transforming activity of mtrIII is located in a 2.1 kb SalI-XbaI subfragment of EJ. DNA sequence analysis reveals four putative open reading frames (ORFs) L1, L2, L3 and R1 in the 2.1 kb fragment. The data from the deletion clones of the 2.1 kb fragment and also by disruption of individual ORFs by restriction enzyme digestion, suggest that a complete ORF L3 or R1 may be essential but not sufficient for the transforming activity. Because significant reduction in transforming activity is obtained by interrupting ORFs LI and L2, these ORFs may be required for the full transforming activity.

3T3 Cells↗

Differential processing of proenkephalin by prohormone convertases 1(3) and 2 and furin.

Recombinant vaccinia virus vectors were used to coexpress mouse prohormone convertase 1 (mPC1), mPC2, or human furin together with human proenkephalin in GH4C1 cells (rat pituitary somatomammotrophs) to examine the proteolytic processing of proenkephalin by these enzymes. Radioimmunoassays performed on high pressure gel permeation size-fractionated extracts obtained from GH4C1 cells and corresponding conditioned media revealed distinct profiles of immunoreactivity for products generated by each enzyme. PC1 produced intermediate sized processing products (3-10 kDa); the major immunoreactive enkephalin-containing species observed eluted at the positions of peptide B, the 5.3-kDa fragment, and free Leu5-enkephalin. PC2 exhibited a more complete processing profile. The major immunoreactive enkephalins produced were free Met5-enkephalin-Arg-Phe, free Met5-enkephalin-Arg-Gly-Leu, free Leu5-enkephalin, and free Met5-enkephalin. Thus PC2 appears to be more capable of generating active opioid units from proenkephalin than is PC1. Finally, furin cleaved proenkephalin to generate peptide B, an unidentified peak between the 18- and 5.3-kDa fragments, and a small amount of the 5.3-kDa fragment. Radiosequencing data verified that the production of the 5.3-kDa fragment by PC1 occurred as a result of a Lys-Lys cleavage. The ability of PC1 to cleave proenkephalin (but not proopiomelanocortin) at a Lys-Lys site implies that the structural context of the paired basic cleavage site may be more important in the determination of cleavage specificity than the particular pair of basic residues at the site.

Amino Acid Sequence↗

Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria.

The prediction of protein structure in insertion/deletion regions (referred to as indels) is an important part of protein model building by homology. Here we combine cluster analysis with data base search procedures. Initially, data bases of representative protein fragments are constructed using two different clustering algorithms. In the HCAPD (hierarchical clustering after preliminary division) approach, all protein fragments are divided into classes with similar anchor region structures (a protein fragment consists of two anchoring regions and a central region). Within these classes the fragments are further clustered using a hierarchical cluster algorithm. The DCANN (deterministic clustering by assignment of all nearest neighbours) approach is a variant of the k-nearest neighbours cluster algorithm. Only geometric scoring criteria are used for data base searching. The main advantage of a non-redundant data base is the ability to provide structurally different fragments during the search process, which leads to an improvement in structure prediction. Both methods have been tested on 71 insertions and 74 deletions with lengths between one and eight residues.

Algorithms↗

The influence of enzymatic cleavage and chemical modification of human and rabbit IgG on their reactivity with staphylococcal protein A.

Proteolytic cleavage fragments from rabbit IgG have been isolated and characterized in an attempt to locate the sites involved in the reactivity with Staphylococcal protein A. The plasmin cleavage product Facb together with the pepsin cleavage products F(ab')2 and pFc' failed to react in contrast to the papain Fc fragment. These data, together with data from unfractionated plasmin digests, in which the Facb fragment remains associated with the plasmin pFc' fragment, indicate that inter-domain interactions are important in the maintenance of this activity. beta2-microglobulin was also shown to be unreactive with protein A. Chemical modification studies employing flurescamine, tetranitromethane and potassium cyanate indicate that lysine and tyrosine residues are not involved in the reactivity of human and rabbit IgG with protein A.

Animals↗

Dissociation and post-traumatic stress disorder: two prospective studies of road traffic accident survivors.

BACKGROUND: Dissociative symptoms during trauma predict post-traumatic stress disorder (PTSD), but they are often transient. It is controversial whether they predict chronic PTSD over and above what can be predicted from other post-trauma symptoms. AIMS: To investigate prospectively the relationship between dissociative symptoms before, during and after a trauma and other psychological predictors, and chronic PTSD. METHOD: Two samples of 27 and 176 road traffic accident survivors were recruited. Patients were assessed shortly after the accident and followed at intervals over the next 6 months. Assessments included measures of dissociation, memory fragmentation, data-driven processing, rumination and PTSD symptoms. RESULTS: All measures of dissociation, particularly persistent dissociation 4 weeks after the accident, predicted chronic PTSD severity at 6 months. Dissociative symptoms predicted subsequent PTSD over and above the other PTSD symptom clusters. Memory fragmentation and data-driven processing also predicted PTSD. Rumination about the accident was among the strongest predictors of subsequent PTSD symptoms. CONCLUSIONS: Persistent dissociation and rumination 4 weeks after trauma are more useful in identifying those patients who are likely to develop chronic PTSD than initial reactions.

Accidents, Traffic↗

Tandem mass spectrometric accurate mass performance of time-of-flight and Fourier transform ion cyclotron resonance mass spectrometry: a case study with pyridine derivatives.

The interpretation of mass spectra is a key process during compound identification, and the combination of tandem mass spectrometry (MS/MS) with high-accuracy mass measurements may deliver crucial information on the identity of a compound. Obtaining accurate mass data of fragment ions in MS/MS reveals the particular problem of mass calibration when a lockmass, which is frequently used to obtain accurate masses in MS, is absent. An alternative technique is to recalibrate the MS/MS spectrum using a reference MS/MS spectrum acquired under the same conditions. We have tested and validated this approach using a hybrid quadrupole/orthogonal acceleration reflectron-type time-of-flight (TOF) mass spectrometer. The results were compared with those obtained under similar conditions on a Fourier transform ion cyclotron resonance (FT-ICR) instrument. We found that the mass accuracy observed with such an "external" recalibration on the TOF instrument in MS/MS is identical to what can be obtained on a similar instrument operating in one-dimensional MS mode using the lockmass technique. However, mass accuracy in both cases is one order of magnitude inferior to that obtained using FTMS, and also inferior to that observed using sector field MS when operated at comparable resolution. Nevertheless, for small (<200 Da) molecules, this mass accuracy was still sufficient to have the "true" elemental composition identified as the first hit in about 70% of all cases. It was possible to elucidate the fragmentation mechanism of eight azaheterocycles containing a pyridine moiety, where the accurate mass data from the TOF instrument allowed distinction between two alternative fragmentation pathways.

Cyclotrons↗

Posterior epidural migration of an extruded lumbar disc fragment causing cauda equina syndrome. Clinical and magnetic resonance imaging evaluation.

STUDY DESIGN: Retrospective case report. OBJECTIVES: To illustrate the rare occurrence of cauda equina syndrome resulting from posterior epidural disc fragment migration documented by magnetic resonance imaging. SUMMARY OF BACKGROUND DATA: Disc fragment migration patterns are generally limited by the attachments of the posterior longitudinal ligament and its associated "midline septum" and "peridural" or "lateral membrane." The majority of symptomatic lumbar disc herniations are noted to be in a lateral position with resultant nerve root irritation. Although caudal, rostral, and lateral migration of disc fragments are common, posterior epidural migration of an extruded disc fragment has been reported only rarely, and only once in association with cauda equina syndrome. METHODS: The patient described in this report presented with an acute cauda equina syndrome. Investigation with magnetic resonance imaging revealed a posterior epidural mass, which was hypointense on T1-weighted and T2-weighted images. Postgadolinium imaging showed rim enhancement of the lesion. The preoperative differential diagnosis included epidural abscess, hematoma, or neoplasm. An urgent decompressive lumbar laminectomy was performed. At surgery, the lesion proved to be a massive extruded disc fragment. RESULTS: At the 1-year follow-up examination, the patient had recovered full motor, sensory, urologic, and sexual function. CONCLUSIONS: Extruded disc fragments may migrate posterior to the thecal sac. Magnetic resonance images of a posterior disc fragment may mimic those of other more common posterior epidural lesions.

Cauda Equina↗

[Sequencing of Cyt b gene fragments and PCR identification of "jinqian baihuashe" (Bungarus parvus) and its adulterants].

DNAs extracted from both "Jinqian Baihuashe" (Bungarus parvus) and its adulterants and original animals of the crude snake drugs were used as templates for Cyt b gene fragment amplification. The sequence data of the fragments showed that the differences of the sequence between Bungarus parvus and its adulterants were far greater than that between intraspecific variations of Bungarus parvus. Therefore, the Cyt b gene fragment was a good molecular genetic marker for the authentication of Bungarus parvus. On the basis of the sequence data, a pair of specialized primers, BuL-1 and BuH-1 was designed for the PCR identification of Bungarus parvus. The effectiveness of the primers were examined at a series of anneal temperatures. The results showed that Bungarus parvus samples could be absolutely distinguished when the anneal temperatures were 60 degrees C-65 degrees C, whereas no incorrect or missing discrimination was found at these temperatures. The results also showed that the powder of Bungarus parvus which was mixed with powders of three other crude snake drugs may be detected by the PCR identification. This indicates that PCR identification may be a new method for examining the compositions of Chinese patent medicine.

Animals↗

Analysis of streptonigrin-induced incomplete chromosome elements and interstitial fragments in Chinese hamster cells using a telomeric PNA probe.

We investigated the induction of incomplete chromosome elements (ICEs; i.e., elements with a telomeric signal at only one terminal end) and interstitial fragments induced by the antibiotic streptonigrin (SN) in a Chinese hamster embryo (CHE) cell line using FISH with a telomeric peptide nucleic acid probe. CHE cells were treated with 0-250 ng/ml SN and chromosomal aberrations were analyzed in the first mitosis after treatment using the telomeric probe. Exposure of CHE cells to SN resulted in a linear concentration-related increase in all of the aberration types analyzed (P < 0.05) except ring chromosomes. Depending on the SN concentration employed, 33-68% of the metaphases contained one or more pairs of ICEs (an incomplete chromosome accompanied by a terminal fragment or two incomplete chromosomes accompanied by a compound fragment). Pooled data from all SN concentrations revealed that 77.8% of the acentric fragments were terminal fragments, 18.8% interstitial fragments, and 3.4% compound fragments. Furthermore, it was estimated that about 80% of excess acentric fragments induced by SN originated from incomplete exchanges or terminal deletions and 20% from complete exchanges (interstitial deletions). These results show that incomplete chromosomes and terminal fragments are the most frequent asymmetrical chromosomal aberrations induced by SN and indicate that true incompleteness is a very common event following exposure to SN.

Animals↗

The growth-associated neuronal phosphoprotein B-50: improved purification, partial primary structure, and characterization and localization of proteolysis products.

A reversed phase HPLC procedure is reported that has allowed the separation of the growth-associated, kinase C substrate protein B-50 [previously purified by isoelectric focussing (IEF)] into three components (1-, m- and rB-50). The minor form 1B-50 (probably a proteolysis product) gave a 24-residue N-terminal amino acid sequence, but the major and possibly native form (mB-50) (and also rB-50 which is probably formed during IEF) appeared to be N-terminally blocked. HPLC also separated B-60, the major proteolysis product of B-50, into three components, and the N-terminal sequence of the major B-60 was determined. HPLC peptide mapping of SAP digests of the various B-50 and B-60 protein confirmed their close relationship, and four SAP generated fragments also afforded sequence data. The amino acid sequences obtained (1B-50, B-60 and fragments) are all found in the recently predicted (based on nucleotide sequencing) B-50/GAP43 sequence (226 amino acids), further confirming the identity of B-50 and GAP43, and helping clarify the relationship of B-60 (starting at position 41 of the predicted sequence) to B-50. Correlation of amino acid analyses, SAP fragment data, and the predicted sequence provided additional information on the length of the translated products, including evidence that the N-terminus of the major (blocked) form of B-50 starts at position 1 (Met) of the predicted sequence.

Animals↗

A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: toward the strict alignment of valid fragments across electrophoretic patterns.

BACKGROUND: Gene expression analysis based on comparison of electrophoretic patterns is strongly dependent on the accuracy of DNA fragment sizing. The current normalization strategy based on molecular weight markers has limited accuracy because marker peaks are often masked by intense peaks nearby. Cumulative errors in fragment lengths cause problems in the alignment of same-length fragments across different electropherograms, especially for small fragments (< 100 bp). For accurate comparison of electrophoretic patterns, further inspection and normalization of electrophoretic data after fragment sizing by conventional strategies is needed. RESULTS: Here we describe a method for the normalization of a set of time-course electrophoretic data to be compared. The method uses Gaussian curves fitted to the complex peak mixtures in each electropherogram. It searches for target ranges for which patterns are dissimilar to the other patterns (called "dissimilar ranges") and for references (a kind of mean or typical pattern) in the set of resultant approximate patterns. It then constructs the optimal normalized pattern whose correlation coefficient against the reference in the range achieves the highest value among various combinations of candidates. We applied the procedure to time-course electrophoretic data produced by HiCEP, an AFLP-based expression profiling method which can detect a slight expression change in DNA fragments. We obtained dissimilar ranges whose electrophoretic patterns were obviously different from the reference and as expected, most of the fragments in the detected ranges were short (< 100 bp). The normalized electrophoretic patterns also agreed well with reference patterns. CONCLUSION: The normalization strategy presented here demonstrates the importance of pre-processing before electrophoretic signal comparison, and we anticipate its usefulness especially for temporal expression analysis by the electrophoretic method.

Algorithms↗

Elucidation of high micro-heterogeneity of an acidic-neutral trichotoxin mixture from Trichoderma harzianum by electrospray ionization quadrupole time-of-flight mass spectrometry.

The high micro-heterogeneity of an acidic-neutral trichotoxin mixture from T. harzianum, PC01, was elucidated using a modern tandem mass spectrometer equipped with an electrospray ionization source, a hybrid quadrupole-orthogonal accelerator and a reflectron time-of-flight analyzer. The trichotoxins appeared predominantly in six possible doubly charged pseudo molecular ions with three different adducts (H, Na and K) as [M + 2H](2+), [M + H + Na](2+), [M + H + K](2+), [M + 2Na](2+), [M + Na + K](2+) and [M + 2K](2+). The singly charged pseudomolecular ions, [M + H](+), [M + Na](+) and [M + K](+), occurred only in low abundance when the cone voltages were higher than 30 V. Additional singly charged fragments, b(12) and y"6 (complementary N- and C-terminal fragments), were obtained in high abundance using high cone voltages. The peak patterns of both singly and doubly charged molecular adducts revealed that this trichotoxin mixture contained several components having 6-7 molecular masses with a consecutive 14 u difference among members in the same molecular adduct series. Furthermore, well resolved isotopic peaks of every doubly or singly charged ions and their reproducible peak intensity allowed the identification of the mixing of acidic trichotoxins 1 u molecular mass heavier than the neutral counterparts in the sample. Tandem mass spectrometric (MS/MS) analyses of various singly charged b(12) and y"6 ions supported the sequence deduction of the major and minor components and also the position of Glu in the sequences of these acidic molecules. The setting of either low or high resolution of the quadrupole mass filter unit together with a suitable variation of the collision voltage for any MS/MS precursor were the tools for extracting a number of mixed components and obtaining the major and minor sequences of these precursor peaks. The nature of the MS/MS fragmentation and the data assignment of three major doubly charged ions, [M + 2H](2+), [M + K + H](2+) and [M + 2K](2+), are demonstrated. Eleven new sequences of both acidic and neutral trichotoxins are reported.

Amino Acid Sequence↗

Two genes encoding steroid 21-hydroxylase are located near the genes encoding the fourth component of complement in man.

Two genes encoding steroid 21-hydroxylase [21-OHase; steroid 21-monooxygenase; steroid, hydrogen-donor: oxygen oxidoreductase (21-hydroxylating); EC 1.14.99.10], a cytochrome P-450 enzyme, have been located within the HLA major histocompatibility complex. Congenital adrenal hyperplasia due to 21-OHase deficiency is a common inherited disorder of cortisol biosynthesis which is in genetic linkage disequilibrium with certain extended HLA haplotypes. These haplotypes include characteristic serum complement allotypes. A series of cosmid clones was isolated from a human genomic library by using a probe encoding part of the fourth component of complement, C4. These clones also hybridized with a probe encoding most of human 21-OHase. Restriction mapping and hybridization analysis showed that there are two 21-OHase genes, each located near the 3' end of one of the two C4 genes. Hybridization with probes specific for the 5' and 3' ends of the 21-OHase gene showed that the 21-OHase and C4 genes all have the same orientation. The 21-OHase genes 3' to C4A and C4B carry T aq I fragments of 3.2 and 3.7 kilobases (kb), respectively. Both of these fragments are found in genomic DNA of most individuals. In DNA from an individual with the severe, "salt-wasting" form of 21-OHase deficiency who was homozygous for HLA-A3;Bw47;C4A*1;C4B*Q0(null); DR7, the 3.7-kb Taq I fragment is absent, whereas hormonally normal individuals homozygous for HLA-A1;B8;C4A*Q0;C4B*1;DR3 do not carry the 3.2-kb Taq I fragment. These data suggest that the 21-OHase "B" gene (3.7-kb Taq I fragment) is functional, but the 21-OHase "A" gene (3.2-kb Taq I fragment) is not.

Chromosome Deletion↗

Fingerprinting method for phylogenetic classification and identification of microorganisms based on variation in 16S rRNA gene sequences.

The paper describes a method for the classification and identification of microorganisms based on variations in 16S rRNA sequences. The 16S rRNA is one of the most conserved molecules within a cell. The nature of the variable and spacer regions has been found to be specific to a given organism. Thus, the method presented here can be very useful for the classification and identification of microorganisms for which very little information is available. To automate the method, a comprehensive computer program called FPMAP has been developed for the analysis of restriction fragment pattern data. The method involves the restriction digestion of genomic DNA, preferably using four-cutters that may recognize 6-9 sites within the 16S rDNA. The fragments are separated on a polyacrylamide gel along with a suitable marker, then transferred into a nylon membrane and hybridized with a radiolabeled 16S rDNA probe. After autoradiography, the fragment sizes are calculated, and the data are analyzed using the FPMAP software. We demonstrate that the method can be used for identification of strains of Streptomyces and mycobacteria. The software is available from our ftp site ftp:¿imtech.chd.nic.in/pub/com/fpmap/unix/.

Autoanalysis↗

Conversion of capillary electrophoresis microchip genotyping data for analysis with Genetic Profiler software.

The collection and conversion of 4-color fluorescent genotyping data from capillary array electrophoresis microchip devices and its conversion to a format easily and rapidly analyzed by Genetic Profiler genotyping software is presented. Microchip fluorescence intensity data are acquired and stored as 4-color tab-delimited text. These files are converted to electrophoretic signal data (ESD) files using a utility program (TEXT-to-ESD) written in C. TEXT-to-ESD generates an ESD file by converting text data to binary data and then appending a 632-byte ESD-file trailer. Up to 96 ESD files are then assembled into a run folder and imported into Genetic Profiler, where data are reduced to 4-color electropherograms and analyzed. In this manner, DNA fragment sizing data acquired with our high-speed electrophoretic microchip devices can be rapidly analyzed using robust commercial software. Additionally, the conversion program allows sizing of data with Genetic Profiler that have been preprocessed using other third-party software, such as BaseFinder.

Alleles↗